I've been on both sides of the deconfliction thing. It can go bad either way...whether or not there is a known issue with one agency or the other.
Agree that the agent going solo is bad policy...and something to be avoided if at all possible for any number of reasons.
I've arrested bad LEOs and not as a member of any internal affairs squad. It feels good to take out the trash...but there's little joy in the larger sense.