When you say that they thought that the two were cysts, I'm assuming that this info is based on an ultrasound? If so, sometimes an ultrasound image may appear like a cyst but it turns out not to be. Also, when the surgeon said that they didn't turn out to be cysts, I'm not sure how she can tell without trying to puncture the cyst. In the operating room, you really can't be sure what something is. You can guess by looking at it and feeling it; but this is only a guess.
If indeed the two lesions are not cysts, they can be a whole list of things, most of which are benign. It can normal tissue, fibrocystic changes (hyperactive tissue), fibroadenoma, complex cyst (cyst with debris inside) etc. I would not worry at this point until the path is out.
Also, some doctors will call you on the phone with results; and some only tell you in person. This is strictly the surgeon's choice.
Good luck. Don't worry too much.