I confirmed the bug on Win10 with 3.5 and 3.6.  "python -m idlelibl -s" prints a prompt*, runs the file and prints any output, and prints a prompt.  It then accepts user input.  When "-c command" is added, it should accept that as user input (and perhaps display it on the input line).  But I get the same error box.  When clicked away, 'command' executes and a third prompt is displayed.

*Another bug. The startup file should run first, before a prompt, just as it does in python, and just as with files run with F5. It would not hurt if [Running <path>] were printed, but not a prompt.  Prompts should mean 'ready to accept input'.  Ditto for -c command, unless IDLE is changed to display the command after the prompt as if typed in.

Warning comes from ModifiedInterpreter (MI).dispaly_executing_dialog, which is called in MI.runcommand if 'self.tkconsole.executing'.  MI.runcommand is used for internal startup code and for '-', '-c', and '-r' on the command line, but not for user '>>> ' and editor code. 

I confirmed that '-s' + '-' or '-r' give the same warning.  Hence the title change.

MI.tkconsole is the PyShell (PS) window instance.  PS.executing is set/reset in PS.beginexecuting, PS.endexecuting.  The latter should apparently be called someplace it is not now.