With the help of MathWorks technical support I'm able to answer my own question. It ended up being a directory in my Matlab path that somehow conflicted with compiling. To test this I reset my path using the following commands:
restoredefaultpath
rehash toolboxcache
savepath
Then I ran the most basic compiling command:
mcc -m test.m
Then I added directories back to my path and checked that mcc was still working.