I don't know what the root cause here, but when I filter out instrumenting for some files, there appears return ... -level 0, so after loading uninstrumented, file gets instrumented anyways. Problematic code is after the comment
# If the "dontInstrument" flag is true, just source the file
# normally, taking care to propagate the error result.
Just put "puts" after "return" in this branch and you will see, that return does not actually return. I don't know how to fix that properly, but I just removed -level and -code from options and it seem to be a workaround.