OK, So I am quite certain that the problem is with having messed with Nesting or Duration of longer clips. If you have a nested clip that is 20 minutes long and you adjusted the entire duration of the nested clip to 15 minutes then the sequence will be 20 minutes long but the work area will be 15.
So you have a cutting board with bits that extend past the working area.
See Screens. I am now Quite CERTAIN This is the "Problem" It isnt really a Problem once you know what is causing it.
But agreed, the Nested duration should not be reflected in the Sequence Work Area.