If you are doing an Upgrade on an existing ship model, and the model has more than one engine attached, this happens:
1) Remove one of the engines by clicking on the engine in the components list and then clicking Remove. So far, all is well and the engine is removed and the space points reclaimed.
2) Select another engine and click Remove. Now you will see something wierd, where the first engine that you removed is put back onto the ship?!?
If you put a replacement engine (like a newer engine type) onto the model IMMEDIATELY after you remove the first one, you will not see this bug. You have to remove 2 engines one after another.
This bug does not seem to affect other component types, just engines.