Im almost 100% certain that this is related, i can reproduce this in 4.13 stable, or 4.13 compiled from source.
Start new project
make blank project
create geometry, 200x200x10 (high)
select geo, copy and past it 5? or so times, stack each piece directly on top of each other, then click build
now try to select an idividual piece.
it wont, it selects the whole thing like it is 1 brush, like so:
Now, you cannot apply a mat to each individual piece like you should be able to (this worked until 4.13 
I really hope this helps. Its making Brushes unusable.