Denial and rejection are two different things. Rejection due to incorrect form is indeed not a big problem in itself. The problem is when somebody is out of status and doesn't have any pending AOS, as they're subject for removal.
Do not rely on any advise by agent. They're low wage workers who do not know the law. VJ is typically more accurate. You can also consult with an immigration lawyer who should reaffirm it.
What do you mean by "missed"? Sounds like a misrep.
Congratulations with your visa approval. Be careful how you answer questions in any potential future application, especially questions whether you ever told US officials something that wasn't true.