I am almost certain this has been reported, but I can't find it in this thread. I'll report it just in case, because it is a rather significant bug but likely simple to fix:
When designing ships, the armor weight is always calculated incorrectly when adding/removing armor or when adding/removing ship components. This happens on basically every ship, and it almost always causes jump engine overtonnages on people building their ships as close to the jump engine max as possible. It is a highly reproducible error and happens almost every time when designing a ship. The armor weight effect can most easily be showed by changing the armor value to a higher value, then changing it back to the normal value, while watching the tonnage.
The workaround for me is to switch to another ship design, then switch back to the original ship design. This appears to "reset" the ship's tonnage display to the actual value that will be used for construction, jumping, etc.