This has been documented as a SOLR bug SOLR-5042, and a patch posted against solr version 4.3. I've relocated that patch back to 4.2.1 and seen that it fixes this behavior there.
If you query the /mlt handler directly, instead of using the mlt component under the /select handler, you can work around this issue, as the handler accepts its count as rows=12 instead of mlt.count=12.