The answer logging is based on the answer rules that are tied to an answer checker in the problem; but MultiAnswer creates "extra" rules that are not tied directly to a checker, so these aren't recorded. The same is also true for Matrix objects that use ans_array, by the way.
I know that the answer log code has recently been rewritten to use the database rather than a log file (as my original 10-year-old code did), but I'm not sure if they have changed that behavior or not. I also know that Mike has rewritten a lot of the underlying infrastructure for the answer checkers in order to make it easier to keep the connection between rules and checkers, so it might be that it would be easier to get this right now. But unless you were running a pre-release version of the system code, then what you are getting is the "expected" behavior (at least in the sense that this is a known issue).
MultiAnswer answer_log logging
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