I've noticed that old ship designs seem to stay in the Mini-Build/Upgrade window, after being obsoleted and even deleted?
I was often just doing a minor upgrade to a ship design but keeping the same ship name. There would sometimes be 3 versions of the same named ship design in the upgrade list, so you'd have to carefully look at the stats before upgrading to make sure you get the right design.
This bug seems worst in the mini-build window.