I have a problem with the removal of material that does as it pleases! One time I have a clean cut and the next time I have what overflows on the photo that remains visible!
I'm attaching a picture of the manip I do!
I can't know where it comes from, especially since it doesn't do it all the time.
This is probably due to the fact that you select the components to be cut and these change in quantity, the new ones are not selected in the selection box.
My version is Solid 2013, yes it's an assembly, yes the floor is a repetition, and yes I have several configurations of my assembly, that's to answer your questions.
In fact I manage to do my material removal well but when I close my assembly and open it again sometimes it leaves me some of the parts that are cut!