Is that save from previous versions? Because since v0.9.0 if your save is from v0.7.0 or an older version you have to start a game from scratch because I cleaned up the code and it no longer checks the same things when loading so the old saves are obsolete.
For some reason, it counts as if you have done the task and since a few versions ago it is "technically impossible". I just tested doing that quest and there is no problem, moreover, you shouldn't be able to get Yuna to level 6 before that quest and that has been impossible to happen for a while now.