Dear Sophia,
I’m assuming, that you are using the BEAM card for your source, and not a source routine. If my assumption is correct, then it is highly unlikely, that it is a numerical artifact.
I would look into the geometry or magnetic field to see of something could cause the problem. You could try to use an Z-Y scoring, to see the tracks of the protons.
Also, if you can share your input file, we could take a look.
Cheers,
David