I have seen this too. For some reason, adding something may take the ship size to 100 but deducting something may leave it at 100.1. For the moment if you find this problem, either remove something and then add it back in or move off the design and re-select it, which will reset the lower value. I will look into what is causing the problem.
I've always assumed that this was a rounding error due to the armor calculation formula being non-linear. I think its frequency went down significantly when you went to fractional armor sizes, i.e. it used to be a lot worse when the granularity was 1 HS.
Do you have any spots on the design screen where adding or subtracting a component calculates a change in hull size, as opposed to having a single routine that calculates size from scratch and is always called when the design changes?
IIRC this could be worked around by switching to a different class in the F5 screen, then switching back - I think that triggers a size recalculation (but I could be wrong).
John