I've never had that happen to me with FMSE.... yet.... well not in SFC 1 homebrew scenarios.
What settings do you have for the game??
Do you run single player missions in skirmish or multiplayer settings??
FMSE doesn't quite use all the AI options for friendly or oposing ships. It isn't possible to preset damage on player or other ships. Neither can specific transporter beam up or beam down objects be set, as in the "Capture The Spy" scenario in SFC 1.
Perhaps FMSE 2 will appear with this facillity included.
You'll have to attach a scenario where this weirdness occurs and see if it can be recreated on someone else's computer.