Whis says that Vegeta was one step behind Goku (although he did mean that in terms of combat, but considering that this is Goku we're talking about here, I wouldn't be surprised if he's above Vegeta, too).
I consider this match up, pretty much the same as Majin Vegeta and SSJ2 Goku so relatively the same.
Whis is extremely intelligent in combat (obvious reasons) not to mention he's almost 2x stronger than them (more than 2x during sparring since they were in base) I wouldn't be surprised if he can point out even the least bit of difference.
Im tempted to believe he could've pointed out a difference similar in the Majin Vegeta and SSJ2 Goku fight.