When I create a drill operation, it's trying to drill the part from the bottom instead of following the MCS +Z axis. My part WCS +Z axis is in the opposite direction of the MCS +Z but this has been the case with other parts and hasn't caused this issue. How do I reverse the side of the part the drill is entering?
My guess is that your two holes have a chamfer on the "bottom" side.
The software, by design, changes the default machining direction from +Z MCS to the direction that matches the chamfer on the geometry. All you have to do is click "Reverse Direction" and your spot drilling operation will come from +Z MCS.
Your screenshot seems to indicate that you are using an early NX9.0.x version of NX CAM that doesn't yet offer the "Reverse Direction" capability. I would recommend that you at least upgrade to the most recent NX9.0.3 MP release (my screenshot is from MP12).