Board Thread:Episode Discussion/@comment-34633327-20171104074017/@comment-10390252-20171106115733

I suspect that guarding Amber was a very unofficial assignment (given the secrecy of Ozpin's cabal). It's possible that Qrow's official mission was to guard the munitions train and to notify the authorities if any White Fang agents were seen hanging around it.

Disliking Jacques Schnee on a profound personal level, Qrow chose to interpret those orders as meaning 'do not engage, only report back'.