The Debian start script for MariaDB, in debian/additions/debian-start and debian/additions/debian-start.inc.sh, runs mysql_upgrade without specifying --skip-write-binlog. As a result, statements contained in scripts/mysql_system_tables_fix.sql will be replicated and fail on the slave.
To be more specific, the ALTER TABLE statements to general_log and slow_log will be replicated, and although mysql_system_tables_fix.sql does disable each of them before running the ALTER TABLEs, these SET statements will not be replicated. When the ALTER TABLE statements are replicated, if the slave system has either log enabled, then replication will break.
I believe debian/additions/debian-start should be modified so that
MYUPGRADE="/usr/bin/mysql_upgrade --defaults-extra-file=/etc/mysql/debian.cnf"
becomes
MYUPGRADE="/usr/bin/mysql_upgrade --defaults-extra-file=/etc/mysql/debian.cnf --skip-write-binlog"
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I think it makes sense. It's hard to imagine that somebody, while upgrading a slave, relies on mysql_upgrade actions coming from master through replication, and without that there should be no other reason to replicate mysql_upgrade activity, while the danger of doing so is obvious.
It would be interesting to know why Li-Bing.Song@sun.com changed the decision, but apparently the discussion hides somewhere in private.