As part of my film studies course I have to do a project on an Auteur and I've chosen the Coen Bros. Problem is I can't think of a question or line of investigation that I should have concerning them.

e.g. Do the amount of references to other films included in their films disqualify the Coen Brothers from being Auteurs

Like that just do able.

Any suggestions would be appriecated.

They have a fondness for the absurdities and ironies of life, and the isolation of each of us to one another. Perhaps you could look at how they fit into the tradition of black humour?
If you were to follow that line of thinking, I would focus on Blood Simple, Raising Arizona, and Barton Fink. These films deal with outrageous twists of fate which seem to tell us that the universe is having a joke at our expense, and use grotesquerie for humour identification.

Good luck whatever you do.
They are definetly auteurs. Borrowing ideas don't mean they don't transform those ideas into their own vision.

I would also include Millers Crossing look at how they twist the film noir, taking elements from previous films such as dark humour and irony.