Seen the following while running an update.php
Notice: PopulateLogUsertext::doDBUpdates: Transaction already in progress (from DatabaseUpdater::doUpdates), performing implicit commit! [Called from DatabaseBase::begin in \includes\db\Database.php at line 3592] in \includes\debug\MWDebug.php on line 300
The problem here is that the DatabaseUpdater starts a transaction before running all the changes, but the maintenance script populateLogUserText.php also has begin/commit in it.
I am not sure if it is okay to just remove the begin/commit because when running the script standalone that does not make problems.