scenariomanager: sometimes binaries do not get stopped, but the manager thinks they are

I sometimes encounter a strange bug, i currently am not able to reproduce:

• I start some scenario
• I do some work (compiling etc. . This sometimes changes the binaries)
• I stop the scenario (often via gui)
• The gui displays all binaries are stopped. If i use the cli to stop, nothing happens (it just prints the default three lines).
• The binary from the scenario is still running and i have to kill it manually.

So somehow my binary is running while all scenario manager tools think it is not.
I don't know what could cause this. (maybe some pids are overwritten)