G code screw ups

I have an airwolf hdx and have been having success with it except for one weird software slicing malfunction. Whenever I have a part which goes up a certain height on the base, then tops off all but a little, (think doorknob protruding on a door) the slicer makes it to where it fills in extra on the top layers of the bigger piece and where it is supposed to be doing infill on the small part, it does nothing. This in turn causes major problems when it starts infilling where it should have been earlier, because there is nothing there for the next layer to bond to. Does anyone else have a similar experience? I am using matterslice as the slicing engine

Its a bit difficult to diagnose without examples. Could you upload the GCode & STL file? Maybe some images of the print as well?