These tutorial details how to make parts (which is what you want to do here)
Fixing the part in core parts would take a pull request on github to fix. Your easiest bet is to do this to get a copy of the part
then right click on it and select Edit Part (new parts editor)
which gets you this
then File->save as new part and just click ok to the default prefix.
that makes a copy of the core part in your mine parts bin. Now you need to right click on that part and select export
that will write a .fzpz file (you get to pick a name!) to the local file system. You then need to unzip that .fzpz file (which will produce a .fzp file and likely 4 svg files.) Using the instructions in either of the tutorials you then need to use Inkscape to edit the pcb svg and correct the pad definition, run it through FrtizingCheckPart.py to check it and then rezip the 5 files in to a .fzpz file. You can then use that .fzpz file as the correct part in your sketches (it will load in to your mine parts bin.) If you run in to problems just post, the procedure is complex and tends to bite without warning.
Peter