I'm having the same issue at least some of the time. I found that some of my older lots where I had used ALT to place things and used resize objects I got the MOO warning even though I hadn't used MOO. I'm also getting MOO warnings on some new builds and I can't figure out why. I took out all mods, cleared the cache etc, and I still had one build the I redid exactly the same on four different lots, one with base game only, and I still got the warning. The house I built after it was fine (and I tested every so often to make sure). I never build with MOO. I don't hate it, but I distrust it and anything that I build always goes into my library with out MOO that way I always have a clean copy of everything I build and I have less fear with issues that come with patches. If I use one of my lots for playing, then I will use MOO if I feel like it/need to.
Whats really sad is that I generally like the MOO warning. Too many creators use it and don't say so in their description and then you download a lot that is an over loaded, malfunctioning, not playtested mess. I do appreciate creators who tell you that they used MOO. Even more if the lot is playtested.