Qt Creator doesn't stop target app running on remote machine in some cases

An built app isn't stopped when "Same build directory" is selected for preference "Stop applications before building:" is selected.
In this case I obviously have an error trying to rewrite running file on the target machine.
However, when "Same project" option is selected it stops the app. Unfortunately I can't stay with the option because at the same time I'm running another project for 2 build configurations and it requires "Same build directory" in order to run another app for both targets.