Hmm... two things come to mind, both from FS1.
When I first played "Paving the Way", I jumped out early-- at the same time the Galatea was warping out, but a few seconds before it fully entered subspace. It made for a pretty cool scene, with the big warship entering the portal in the background. Then I got to the debriefing and Admiral Shima's screaming at me... "The Galatea was destroyed, and YOU are to blame!" After briefly wondering how 2 Shivan bombers could unload 18 Harbingers in 3 seconds on an Orion traveling 450 m/s, I decided to just avoid the situation entirely in the future...
Later I was replaying the main campaign on Easy, and on the mission with the shield prototypes (Hammer and the Anvil?) I decided to take a few early shots at one of the then-friendly HoL fighters before it went hostile. After five shots all the green dots on my radar turned red, Alpha 3 shouted something about treason, and I learned the fun way what Traitor Mode was.