When it says "le colonel" doesn't the "le" imply the colonel is a man? So "The colonel covered "her" men" would not be a correct answer.
it could be that the word colonel is always masculine while there can be female colonels, this is something that definitely happens in my language (spanish)
The men covered by the male colonel might have been someone else's men -- perhaps a female officer's.
I am not sure why "the colonel covered up for his men" is incorrect. "covered up for" is one of the word hints.