I once had several mysterious issues with 16.04 and a custom shell-wrapped sudo installed by some IT guys to the point that I installed "stock" 16.04 and *not* the IT guys' provisioned stuff. After using the stock install *without* specially provisioned software things worked much better (like they are supposed to!)
I think it makes sense to try this out on a stock install without mucked up versions of system utilities. It's possible that these are in fact bugs in pybombs as a result of corner cases, but without being able to reliably reproduce the corner cases it's pretty difficult to fix those bugs. In my case attempting to use pybombs with the specially provisioned software exposed bugs in the specially provisioned software (which was a good indicator to avoid using it).
Cheers,
nw