When upgrading a prior ship design I had a problem with being unable to remove items from my design to make room for new items. When I clicked on the item in the ribbon and selected remove, the item would not be removed. I could go into the design and select the item (in this case an engine) and could remove it from the design, but the engine icon would stay in the ribbon.
The end result was that I aborted the design modifications and created a new design from scratch. Only tried this once in my game and have not tried it since. However I did think it might be something you might want to look at.