From Matlab-related website:
"Contourf has a longstanding bug in handling internal masked regions; I hope you don't run into it. Both Mike D and I have tried to figure out how to fix that bug, but so far without success."
This appears to be what I'm seeing, so I'm hoping someone has experience overcoming this? If not I'll have to remove a few pixels from the matrix I use to populate the plot so that it doesn't interpret the masked internal areas as internal... That's a non-ideal clunky solution, though, since I'll have to do so manually every time I get new output.