Yeah they were the only two in the tank at the fish store so I figured they were at least a bit used to each other.Were they the only 2 clowns in the tank at the LFS?
If so, and if they were together for a little while, they certainly may have, and if so, the female(larger one) may just be annoyed by the cramped conditions.
But, to be safe, when you add them to your tank, you might put the larger one in an acclimation box for a few days and let the smaller one free to roam the tank. This *could* help with aggression since when you release the larger one, it will be the "newcomer".