I'm having the same problem, i prime the breaching charge and when i hover the cursor over different parts of the corvette they light up, but the cursor is showing the crossed out icon.
As this is my first playthrough with FitH, i thought i just didn't know how to use it, but i've tried everything i could come up with and no luck.
Also, i think i couldn't breach scouts either, but i'm no longer sure if i tried it or just assumed they were to small to breach.
save game:
https://dl.dropboxusercontent.com/u/11702530/assault%202.sav