Exited station didn’t have IC scanner

I took the Ishikawa railway from around Kanazawa, tapping in with an ICOCA card and transferred on the platform to a JR west train, exiting a station somewhere around Toyama which did not have a card scanner. The gate staff told me to pay the whole fare in cash and gave me a certificate of payment. He told me to go to the next big city JR station to get the card cleared.

I then rode my bicycle to Gifu over several days and presented the certificate and card to the gate staff at Gifu Station. But the staff said he can't do anything and told me to go back to Kanazawa at an Ishikawa railway station to fix it. I told him I wasn't going back to Kanazawa. So he told me to go to the nearest JR west Station, Maibara, something about the card being ICOCA which he can't fix.

So I went to the ticket office to get a second opinion and they told me to go back to the gate.

The staff at the gate changed so I asked again and the lady simply took and kept the certificate and said it was done.

The card history says entry Ishikawa, and instead of exit, it says window with an asterisk Gifu. Does that mean it's fixed?

Why did 2 staff give completely different responses (made me spend an extra hour in different lines)?

What's the correct way to transfer between different rail operators that don't have separate gates and share the same platforms?

Should I always tap out when transferring between different operators and then come back into the gate?

How can I tell when a connecting line doesn't have scanners at the subsequent stations?

Seems simpler not to use the IC card to avoid this happening again.

My guess is that because it happened to you in the JR West area, the person in Gifu, which is in the JR Central area, thought he could not do it. Not sure.

In any case, it is your duty when using an IC card to know whether you can use an IC card for the journey traveled. I don't like your attitude of complaining about time lost, while you are wasting the time of JR employees with your mistake.

The valifdity area of the various IC cards can be looked up online. For example, I quickly found this when searching for "Icoca area":
https://www.westjr.co.jp/global/en/howto/icoca/area/

Besides stations without IC card scanners there are also other trips that are not possible with IC cards, such as crossing over from one to another card's area (e.g. Icoca to Kitaca). Most of these additional rules are explained here:
https://www.japan-guide.com/e/e2359_003.html

The simple explanation is that you went out of area and normally you need to get your card "fixed" in the area you entered. Not all issues like this can be fixed out-of-area or by a different comany. For example, if your card is messed up on a bus fare, you may need to return to that bus company so the card works on transit again.
I've done this a couple of times (most recently in Kagoshima). Certainly not all of the country is covered and especially for stations without IC ticket gates - there are hundreds of those.
Even if your card is messed up for transit, you can still use the remaining balance for shopping/other things.

Why did 2 different gate staff at the same gate at different times give different responses? One staff clears the card in 5 seconds without questions and says everything is fine, and the other staff saying they can't do it.

Why are there no barriers or gates at these stations between different rail companies that have different ticketing systems, and what are you normally supposed to do when transferring between them when they're on the same platform or the next one over with only a staircase away?

There seemed to be gates at the transfer station but it's quite a long walk to get there from the platforms. Are you supposed to use paper tickets on both segments? Get a paper ticket at the starting gate of the first rail company and then get another paper ticket on board the second train of the second rail company?

Well, I wouldn't be too harsh on the OP.

Yes, my guess is that it's the difference between JR West company and JR Central company, AND the fact that the "once-united government-operated JNR Group" is not catching up with the diversity of traveling styles even after 37 years of being separated into West, Central and other JR commercial companies.

I also don't really think that it's the "duty" of a traveler to know everything about this confusing system. But then, you have to understand that some JR personnel know better than others.

Should I always tap out when transferring between different operators and then come back into the gate?

There are stations where it's simply not possible to even ask. But if it's during the day, there are multiple-language official phone lines like JR East Infoline that can also try to help you about other JR company areas.
https://www.jreast.co.jp/multi/customer_support/infoline.html

The other thing I try to keep in mind is that a lot of train personnel, especially with JR, are more like train geeks than service people, and vice versa. And you can also report your complaint to phone lines like JR East Infoline so that the whole JR group can improve in the future. I wouldn't say that other countries are better, but if the system improves, everyone including the workers would be happy.

Why are there no barriers or gates at these stations between different rail companies that have different ticketing systems

Trains, all over the world, were originally just a means of transportation that were way better than walking or horse-riding or even bicycle-riding in the rain. In the beginning, the railway organizations were literally public-run instead of being commercial corporations. A lot of no-man stations get crowded twice a day when locals commute to one certain high school or work place. These stations are designed for places where everybody knows everybody.

And the JR group in general is not rich at all. Like any commercial corporation, each JR company tend to spend their whole fortune on things that are more profitable. Typically, the smaller remote stations AND trains are left out. But then, the smaller stations can still manage for some years without problem, because most users (who are the local villagers and commuters) only ride the same route over and over again.

I don't know what the purpose of your travel is, but if it were fast-travelling and if I were you, I'd try to think that I failed to do enough homework. And if it were slow-travelling and if I were you, I'd try to think that I was fortunate enough to literally step off the beaten track and being able to bring home a great travel story.

I hope it helps.

good morning and sorry to hear about the unpleasant experience
nevertheless reading Uco san's response put a smile on my face
so hopefully it does the same to you too

i am a bit vague as to your exact entry and exit stations
"from around Kanazawa" and "somewhere around Toyama".

so as a quick guest, assuming you were using IRいしかわ鉄道 Shikawa Railway
transiting to a JR West train, exiting perhaps at
JR West 速星駅 Hayahoshi or 越中八尾駅 Etchuyatsuo
at which neither stations are ICOCA enabled.
https://www.ishikawa-railway.jp/ticket/icoca/index.html#Area

A few days after the bicycle marathon, you were physically exhausted and
visited the nearby 岐阜駅 which is under the JR東海 JR Tokai
and not JR West who issued the ICOCA

assuming above is a close guess, to answer your question
"Does that mean it's fixed?"
it depends on whether you could use the ICOCA for any transport thereafter

if YES then we have to gratefully thank the JR Tokai staff
who has no obligation to fix an ICOCA card issued by JR West
you were indeed blessed to come across someone so kind and helpful

the first staff would have just followed the SOP in place and provide recommendation
by the book, ie. attend the next JR West station on your way to resolve the any ICOCA issues

i dont think you did anything wrong by transiting between railway operators
it is not uncommon that non major stations are not IC enabled
and usually not a big deal to pay at a manned gate when such technology is not supported

if you are traumatised by the experience for some reason
please google the entry and exit stations prior to your trip
and confirm whether both support the use of IC card eg ICOCA

i personally would not bother
why give up the beautiful opportunity to interact with local Japanese
and make this an amazing part of your daily life during travelling

as to your profound realisation that
"Seems simpler not to use the IC card to avoid this happening again."

i would beg you to give the IC card another chance
its benefits and convenience far outweigh any limitations
just see it as a boyfriend and / or girlfriend
even though they do introduce imperfection & complication
and sometimes disappointments and headaches

on a more serious note
it is never too late to pick up みんなの日本語 Minna No Nihongo
you would very soon be empowered to ask the relevant JR staff any questions
in relation to the use of IC cards and provide friendly feedback promptly

have a wonderful trip ~

Certainly not trying to be hard on the OP - quite simply there are no physical signs of where the boundaries are and it is easy to travel (and transfer) from one company to another (like JR to Odakyu at Shinjuku when simply heading to an exit).
And, regarding service people, it is true that they are not all knowing - they make mistakes, or might not know the rules and areas that you travelled through.
I had a weird interaction just yesterday - I was 100 yen short on my card, the fare adjustment machine was out of order, the attendant couldn't take cash, and the re-charge machine refused to recognise my card so the attendant let me leave with my "bricked" card. I planned to fix it when returning a couple of hours later. Returning said couple of hours later, attendant had gone, pushed through to access the now functioning fare adjustment machine, did the top-up, tagged out, then back in and all fixed. But certainly not obvious.