Hello,
It's been a while but I decided to up this thread instead of creating a second one since the problem persists. I looted a cottage on a custom game (the cottage where the old couple lives) and the progression is stuck at 91 % even though there is nothing left to loot and the orange text describing the quantities of loot present is actually not there anymore, confirming my point that there is nothing left to loot.
I'm not sure how the percentage is calculated. For example, there is one instance where the loot doesn't appear until you read a note saying that the previous inhabitant hid gun parts in the garden. Either way, I do not think there is anything hidden in the cottage.
Furthermore, I am wondering if killing the old couple and looting their corpses contributes to the total percentage. But I would rather not try it until I either get confirmation that it does or I find a way to back my save
EDIT: After reviewing the post I made over a year ago, I realised that I was wondering the exact same thing about whether killing someone counts towards the loot percentage, and I never got an answer, lol.