Not easy. Stop letting engineers do drawings.
Suppose a quick check is just to use the quick select command and see if entities are bylayer.
It's hard, I had the same problem, although it's got better, as we implemented cad manual 5 years ago, and engineers are only allowed to do minor cad. That has stopped the bylayer problem.
Also we have lot's af layers for just about every services, high level, low level, underground etc.. so it is easy for engineers to use the system.