I have never been on provera so I don't know. I do know, however, that there are many reasons why someone would miss their period. Stress, weight loss, etc.
Did the doctor do a pregnancy test? It sounds like you are not on birth control now, so of course if you have been having sex you could be pregnant. But if the doc did a test I would trust the results. And if you have been pregnant for three months, the doc would definately be able to tell easily without much doubt.