Ok let me see if I got this right:
1. You entered, used 2 stones and got a total of 118 minutes.
2. You then immediately exited the abyssea zone.
3. You reentered and got visitant status again without adding more stones, which would give you 118 minutes - i.e. 2 minutes less than max time.
4. You went about your business in the abyssea zone, and with 20 minutes remaining you added another stone which only added 2 minutes to your total time.
If that's what you did, then it's working as intended so to speak. Doesn't matter that you did exit, you still had 118 minutes when you reentered and got visitant status again. So yes, extending time after that would only give you an additional 2 minutes. And exiting when you did makes no difference, you'd have to have 87 minutes remaining (or less) when getting visitant status, to get the full 33 minutes when extending time. Now, if you had exited when you had 20 minutes left instead, you could have reentered, gotten visitant status chosing not to use any traverser stones, and then extended time and received an additional 33 minutes.
It's not a bug, it's always been this way. Your total time remaining when getting visitant status is what determines how much time you will receive when extending.