This will be rectified in the newest version as you will have an inspector tab. This will let you see that you have a break point assigned that isn't in view. The only other tip I can give is to always maximize your RLM screen when working on it.
First, the screen was always maximized. The property window always covers the break point bar so it is always impossible to tell by looking at the screen if break points have been inadvertently set. Likewise it is not possible from within RLM to clear these break points.
I will bring this issue up with support to see if they have a satisfactory work around - and I suspect one exists using a quick fix in custom.css.