If the main thread executes the assertion on command counts after the NITL thread has successfully run killOperation for the request that timed out, then it will see one more successful command than expected and fail. This can be deterministically reproduced with a 100ms sleep here: https://github.com/mongodb/mongo/blob/0a68308f0d39a928ed551f285ba72ca560c38576/src/mongo/executor/network_interface_integration_test.cpp#L873 

Make the test shutdown the NITL before asserting on command counts to ensure it is done with all work.