Ah, thanks ems.
Yes, if someone said something which you didn't catch, it would be more common to say, "Could you repeat that please?", where "that" means "what you just said".
Using "Could you repeat it, please" is more likely to invite the response of "repeat what?" than is "Could you repeat that, please?"
There's one exception I can think of. That is where you have been asked for information.
A: Please give me your address.
B: <Something unintelligible>
A: Could you repeat it please?
Here, "it" refers to "your address", not primarily to "what you just said" - even though they are likely to be identical in this case.
But, salitre, if you are going to take a few words out of the context of those examples, you would be able to make the case that saying anything in English is wrong!
The claimed error is quite clearly, "Could you repeat it please?", not "repeat it".