The cottage isn’t a house, it’s more like a dacha.

cottage is like дачный дом

cottage is like дачный дом

By your American standards it might be a dacha, but for many UK people it's just a an old(-stile) house (low ceilings and doors, exposed beams, sometimes thatched roof etc.) where they permanently live.
https://www.onthemarket.com/for-sale/cottage/uk/

That’s true enough, and I do often think and express myself like an American. However, having said that, I know the word дом has a very broad interpretation, which can range from a simple home to a whole building of apartments. I just thought that perhaps in a language as rich as Russian one might have the lexical wherewithal to narrow this down to something as rural and cozy as a cottage. Apparently not.

Depending on the context (since the interpretation of the "cottage" is broad), one more translation is possible. I mean "коттедж" - a purely Russian word. :)) But, without knowing the context, I'd also go with "дом" as a more general word.
More than that, my translation would be Но что-то было не так со всем домом. To me, во всём доме would mean only its interior, which isn't the case here.

Very interesting. Thank you for expounding on this.

Anytime!