Stay away from "When you are saying that" (unless you intend to refer to something the speaker is doing at the same time, as in: "When you are saying that, you aren't looking at me."). But, there are alternatives, especially if you want to refer to something said in the past. You can start with "When you say that . . " (which implies the speaker has said it before). Or, if you're want to refer to something that just happened, you can say, "When you just said that . . " Or, if you want to refer to something the speaker says often, you can say, "Whenever you say that . . " To be more polite, try: "I am sure you didn't intend to say anything bad, but . . " (for something said once), and "I'm sure you don't intend to say anything bad . . " (when the speaker has made the remark before). I hope I haven't confused you!?

Yes, you can use "when you are saying that" about someone who says something repeatedly. For example, imagine a friend you have is in the sales profession. He uses the same speaking line to sell what he sells. Maybe he says something you disapprove of. "I'm sure you don't mean anything bad when you are saying that, but maybe "this" would be better." I hope that helps.

The simplest answer is - Yes, you can say "when you are saying that". It is completely understandable and acceptable English.