Pokémon stuck at Gym. Not returned after kicked out of Gym. No coins either.

Try closing and restarting app? I've noticed a lag sometimes before my coins register.

I've heard that this is a thing, but I've never experienced it. Just try to not stick anything in a gym that you really want back.

I have read in SilphRoad that this is a known bug, albeit a very rare one. Many people have tried to contact Niantic about it but none has reported a successful fix.

Yes. Two of my pokemon (both are Snorlex) are stuck at different GYMs even thought both of GYM have been changed color for many times. The 1st one was stuck two days after new GYM system, while the 2nd one just happened three days ago at a GYM nearby my home. But I have not contacted Niantic yet.
One possibility is that this bug (or glitch) may already be there for long time. However since in previously GYM system, the pokemon(s) will bring coins everyday, none of player will care whether it was stuck or not. Now it has no coins, no use (and just occupy the poke storage if they are about to meet the professor).

It is a known bug. On TSR the Niantic reps have acknowledged that the developers are aware of it.
Apparently, if you looked in the gym you would not have seen your mon, although it would get the defender badge showing in your pack.

I will post a link if I find the source.

My situation sounds slightly different: I've had a Snorlax at a gym for 15 days. I don't even see any more red on his motivation meter. It's been like that for 10 days. Either somebody is keeping him on life-support, or there's some sort of glitch holding him back.