This only happens if a metal propeller is present. Most notable with Tornado (Modern Weapons Pack).
Acquire an advanced metal cockpit and click "Craft" in the respective screen. Nothing will happen. Now acquire a metal propeller and try clicking "Craft" again. Both items will disappear from the inventory. For the record, it removes all required recipe items it can find in the inventory up to the necessary amount. (It will only remove 8 out of 10 gray dyes, or 2 out of 7 wings, for example.)

Thanks for reporting this, I can imagine it's claimed quite a few items from people!