Doesn't matter how many beds are free nor the size of the settlement. This situation started after Preston got to max relationship level with me and I had options for Dogmeat, Preston, and Codsworth who at the time were all together in Sancutary. Now with 4 more companions every single one of them has to be at a different settlement which has gotten ridiculous. Not only this, but Preston won't even accompany me. I'd like to have Piper stay at Santuary so I can get the lovers perk for sleeping with her, but instead I have to travel way out to some far flung settlement.
The way it works is, when I go to switch companions or just part ways with them, Santuary is greyed out along with other random Setttlements depending on who is where. Annoying.
I'm on PS4 and have 50+ hours in the game