cplaster
commented
3 weeks ago I encountered this same problems a few months ago, and it seems that it has to do with how hint generation is handled for impa's house specifically. I fixed this on my builds by essentially skipping this check (see here). I didn't submit a PR because this probably isn't the right way to handle it. All other hints seem to still be correct, I suspect you just won't see hints that have to do with the location. Hope this helps!
Interior entrance shuffle currently fails while trying to place the second entrance to Impa's House after placing the first one as a result of cowsanity also being on. Turning Shuffle Cows off allows Interior shuffle to succeed.