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In "A Good Man Goes to War", the Doctor said, "No flies on the Roman," when Rory identified the cot as a cot.
The expression "[There are] no flies on" someone simply means that the person referred to isn't slow -- usually meaning not slow on the uptake. The Doctor called Rory "the Roman" because of his centurian outfit.
In this case, the Doctor was being mildly sarcastic, since Rory had merely stated the obvious.