I made a very big mistake, in some instances there will be two popovers on the screen at once. What is the probability of getting my app rejected?
Generally, a popover will be dismissed if you tap outside of it, so unless you are using a popover inside of a popover, the situation you describe is impossible. If you are nesting popovers, I suspect that you are correct, it may get your app rejected.
From the iOS Human Interface Guidelines:
Ensure that only one popover is visible onscreen at a time. You should not display more than one popover (or custom view designed to look and behave like a popover) at the same time. In particular, you should avoid displaying a cascade or hierarchy of popovers simultaneously, in which one popover emerges from another.
Apple will reject any application that displays two distinct UIPopoverControllers onscreen at once (many people I know have run into this). At first, they let a few applications on the store that did cascading popovers (a popover within a popover), but this language seems to have tightened up, so I'd expect them to not allow this now.