Sorry for my ultra late reply, but thank you for checking!So, the third treasure in The Witch's Shop map seems to be the old container that you are supposed to dig up by using ground bomb while with the teacher. You never collected that apparently. However, collecting it now won't do anything apart from give you the Old Container item that cannot be opened outside of the tutorial sequence with the teacher.
I'll have to do some testing, but that seems to be the missing data. (Not even sure how it was skipped... though I can only go back to version 0.20s at the earliest)
As for the other map, not sure yet. Pretty sure 100.0% on the Forest map is possible without the crystal room chest.
EDIT: Wait, just found v0.09n...
EDIT: Given the content difference from 0.09n to 0.20s, saves from before 0.20s should not be used in later versions.
...I honestly had no memories of what I did or what I missed before because its just been so long since I last played (and so long too for the first play before those) so... Welp, I'm stuck I guess? Sad :'(
Thank you again for the help though, I really appreciate it!