The most likely answer is that there's a room somewhere that you haven't gotten everything from, or there's a type of item (like broken barrels) that you're missing.
I've done that quest probably over a dozen times now, and I tend to miss either the closet next to the coat check, the larder beneath the kitchen, or the rooms in the west wing of the second floor.
I'm actually having the same problem. I've done the basement under the kitchen, all 8 rooms of the guest house, the closet south of the library, and all 3 other bedrooms in the west wing. The only areas I can think of that I haven't scoured are the servants' quarters (inaccessible from the outside), the second floor east wing rooms (inaccessible due to giant hole), the room just north of the office (inaccessible from blocked door), and the master bedroom (PC just unwilling to do anything there).
I'd previously gotten the trophy for killing rats at the start of the game, so I had covered at least most of the accessible areas by that point, so I'm not sure where else I can go now.
At this point, I've resorted to stepping on every floor crack on the first floor just to see if there's a hidden basement full of debris I can fall into.
I can definitely tell you there aren't any secret or inaccessible rooms counting against you. If you aren't missing any rooms, chances are you're missing a type of item that looks intact-ish, like the stools (overturned or not, you can pick all of those up) or - if you've actually managed to do basically everything - just the table in front of Melissa (which could be getting overlooked because she's using it) or the handful of bits in the gallery since it's easy to mentally cross it off as being part of the same map where you've done everything else.
Though if you're that close, you should've already gotten some kind of notification to talk to Phoebe from Ella. Even if you're not getting the "you're completely done" notification every time you walk into the main room of the first floor, there is a leeway gap to try and prevent situations like yours so you can go into the Deep Wilds to finish gathering the wood you need rather than going insane trying to find the last straw of hay that's left of the haystack you already cleared out. The trophy only cares about whether you skipped repairs or not, so you won't miss it by going to the Deep Wilds early if the option is available.
