It sounds like you are using the CPU-external.tst file.
The problem is that the CPU-external.cmp file that's on the site appears to be an old version. If you look at the CPU.cmp file you will see that on line 33, and a lot of others, outM is ******** meaning that it's value is undefined.
This happens because the output of the ALU is irrelevant during A-instructions, and in fact can be different depending on how you implement your control circuitry.
Use the CPU.tst file instead; it's also a better test since it also tests the D register.
Here are updated files it you want to try them:
CPU-external.tst CPU-external.cmp--Mark