I'd think this is just a matter of lyrical freedom, keeping rhyme intact whilst emphasising the fact that one mph transgression is only just a reason to pull him over.
See also this close reading from a lawyer's perspective from the article Jay-Z’s 99 Problems, Verse 2: A Close Reading with Fourth Amendment Guidance for Cops and Perps:
You was doing fifty-five in a fifty-four . . .
All drivers—not just those smuggling drugs—have reason to complain about what they see as arbitrary speed enforcement. Drive down a highway with a marked limit of sixty-five, and you’ll see that virtually every car is speeding. The cultural norm we learn as drivers is that anything within ten miles per hour of the posted limit is okay. 
But as a matter of law—which is what matters for the suppression
issue—if you’re even one mile per hour over, that’s sufficient to pull you over, write you a ticket, and, if the officer chooses, to arrest you. 
Neither arbitrariness nor pretextual motive is relevant to the validity of the stop if it is based on probable cause that you were in fact violating the traffic law. 
Jay-Z explains the line as “another way of saying that we’re being pulled over for no good reason.”  As numerous commentators have observed, the number and scope of traffic regulations is so extensive that the police can in practice find a perfectly legitimate traffic-law basis for stopping any car they choose, just by following it for a few blocks.