That's weird.
Regarding the resistor, it's either a bug in the CAD software itself, or the board manufacturer has maybe used the wrong stop layer (which controls where the
green mask gets placed) for the top and bottom sides maybe? - you would need to check the entire board to see if that is the case).
What CAD software did you use, just out of interest?
Regarding your large pad, did you create the part yourself, or was it part of the CAD package library? If you created the part yourself, was the
pad actually defined as a pin, or as just an unconnected square of copper? If the latter, then you would need to have manually drawn over the
square with the stop layer, to ensure the copper was not covered with the green stuff.