When debugging, if your program stops at a breakpoint, and you want to get rid of the breakpoint for the future, you can't just double-click the breakpoint to turn it off. Well, you can, but if you do, your program will crash the next time through this point.
Instead, you need to open up the Breakpoints window and remove it there. Then close it and continue running.
Also, make sure to remove all breakpoints when you save your project for the last time. Otherwise loading a large project can consume all your user resources.