You've missed out a super important detail: which version are you playing? I'm gonna assume 0.23c like in the OP
For the Witch's Shop area, make sure you have followed all dialog paths and have searched Laevigata's Atelier.
As for the crystal room, that treasure marker is left in for old saves as the item was removed in a previous update. As such it does not count towards 100.0% completion for the map. (Old saves get to have that marker checked off still if the item was previously collected)
P.S: The break room doesn't count towards completion.
Thank you for the response!
I actually am using an old save (played since the very oldest version where we can only do tutorial without reaching her house) which I last played last year (on last year's version) that I loaded using the newest version that they shared on their site (0.23e_2 iirc)
But yeah for some reason that marker is not checked at all (I just checked the wiki and its the Statue Amulet yeah but iunno why its not checked...)
I also checked the wiki for the Witch House and yep I couldnt find anything else other than the item in Laev's atelier and the one puzzle underground... Why is it listing me as missing one...?
TLDR Yeah I'm playing on newest version on their site (0.23e_2) but using a very old save (that started from a very primitive version but did last played on last year's version)
EDIT:
I've searched Laev's atelier (both the one where you can craft and alchemize things and the one below the well with a single item box) but it still wont register a 100% (still 66.67%)