The cyclons aren't all perfectly identical, and they clearly have differing experiences and personalities, which means they'll have slightly different mannerisms, speaking patterns, walking styles, etc. If you know someone really well for a long time, you can tell that the person walking up behind you is them based on the sound of their footsteps.
I think, if it was just a short conversation or something, I'd let it go. But he frakked her against a wall in the locker room place. x.x
It's not like he had zero reason to suspect Athena of ever being anyone but Athena. There's eights wandering around all over the place, and most of them have the same haircut and clothes.
But... whether or not the mix up is his fault, Athena could still get real ticked off. If it's a cylon thing, she likely can't imagine not being able to tell the difference.
On the other hand, Athena has bigger things to worry about than all of that, seeing as her holy-****ing-grail of a kid is in a box on a raptor god-knows-where in the universe...