Not sure if this has been raised before, and it's not the worst bug in the world but I notice when you use Window -> Split to split the current file into two separate scrollable views, the code coverage dots only appear in the lower view. If you then click Window -> Remove Split to go back to single view, it removes the lower view and the coverage dots have disappeared completely. Closing and re-opening the file brings them back again.
Fairly minor really but I use split screen quite regularly and sometimes I forget this bug so I start wondering why NCrunch has disappeared before I realize it's just the dots have gone!