When exiting the debugger prematurely, (ie debug | stop debugging from a breakpoint or abort on an exception or assert), more often than not the keyboard interface is broken. The only keystrokes the IDE recognizes would be the short cut to a main menu, and while the menu is displayed, then any keystrokes seem to flow into the active window. I have to quit and reload Visual Studio to fix this. No other software is affected.
You don't specify what type of program it is, such as console program, but the program is probably doing something it should not do.
Check the Task Manager to see if your program is still shown as a process (in the Processes tab) after you stop debugging. If it is still there, then that is nearly certain proof that the program is doing something it should not do.
