When designing ships in a single player game, there are no engines available on the tool bar. Ships already with engines can be loaded, modified and constructed normally.
Outside of a single player game, engines appear normally in the tool bar.
Weiiird. I'm afraid I can't reproduce it though. Sanity check question: you were editing ships, not buildings? Can you post a screenshot?
After doing it to me twice in a row, it is now working correctly. I've tried to get it to reproduce again, but whatever was causing it seems to have vanished.
Your computer is probably haunted.