So I've run into my first issue. I was playing Dark Omens with the objective to wipe out the Borg base (just filling people in in case this is important) and while I had done so the Borg had started construction of a new building. This was at 0 percent before I wiped them out. I think this is why the level was not progressing as it still registered as there being some Borg base left even though I couldn't target it.
Anyway I figured no worries and just hit the level skip cheat.
This is enter followed by "kobayashimaru" and then hit enter again. Instead of skipping the level this seemed to chuck me out of the level.
Any suggestion or advice?

Hi all the issue has been solved. The next issue is the Klingon campaign and this is why it went back to the level screen. Apologies

This was a bug for that mission that had a high variable of repeating as you played through the Fed campaign multiple times. Your choice to skip the mission was in no way a dishonorable act. Cheers