"There's the rub" is a Shakespearean phrase used during Hamlet's famous soliloquy. Basically, it means, "that's the problem."
In this case, the problem is that I've played perhaps a total of twelve rounds of fighting games in my life, and eight of those were with the Fighting Is Magic demo at Everfree NW. Of those eight rounds, I only won one fight: Applejack vs. Rarity, I think.
I had never noticed that about good old Rottingham. That makes the scene even funnier.