I have upgraded from PyCharm 2017.3 under Ubuntu 17.04/10 to PyCharm 2018.2 under Ubuntu 18.04.
Running my app from the Debugger (i.e. not attaching to a running process, if it makes any difference), on the old system, when I hit a breakpoint the debugger window correctly became "up-fronted" on the breakpoint lint. (At least sometimes/most times it did; occasionally PyCharm seemed a touch flaky about this.) Under the new system, the debugger window always remains behind the application window. The application window is provided via Qt/PyQt, though that should not matter.
Following a PyCharm post/bug report I found elsewhere, I have tried altering:
File > Settings > Build, Execution,Deployment > Debugger Page
to try switching Focus application on breakpoint off, and also Show debug window on breakpoint off too. neither of these has altered the behaviour.
I would have thought it is the Show debug window on breakpoint setting which is at issue. I find neither on nor off makes any difference?