I would need more information to exactly answer you, but if I understand you right, it is possible that all but two holes are positioned OFF of the face of the body you are drilling. If this happens, I believe UG might still create the features, even though they fall off the part, and are actually non-existing (although I was not able to verify that in NX1). Another thing to check is if they are created inside a body, and are actually "swallowed up" by the body.

Thank you Demco, I think other holes are positioned inside parts body, the problem maybe the UG is not supposed to show them all, will that happen? and I will verify my design again to let you know.

Is your instances being suppressed?
Perhaps that could be the reason it doesn't shows up.

thanks hocky. Unfortunately, it's not suppressed, I found that holes are not perpendicular to X-Y plane, and you know that instance function ask for x offest and y offset, I don't know if this belongs to an error or unperfection of software. That's all I neglected. Sometime, I need to be more patient. Thanks for all advices.