The issue is based on how much time you spent previously without zoning. When you enter the zone, you have X amount of time leftover. At most, you can add 120 - X to your time; let's say you had 60 minutes, so you can get 60 more minutes. However, once you've hit "120", the game reads you as having spent the maximum amount you can on this visit. If you're down to 90 minutes and try to spend a stone to get 30 more back, you won't get a single minute back, because you've "maxed out" the amount of time you can get with stones without zoning. It's probably not a bug, likely a "working as intended" for people to be forced to zone and reset their lights. Something time sinks something something...

Anyway, the short of it is that the most time you can get without zoning out of the Abyssea area is 120 - X, where X is your time remaining when you entered the zone. It's stupid, but it's been there for a long time.