Zdá se, že je to opraveno v 10.1.22.
Server version: 10.1.22-MariaDB-1~xenial mariadb.org binary distribution
Copyright (c) 2000, 2016, Oracle, MariaDB Corporation Ab and others.
Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.
MariaDB [(none)]> select 'a%b' like '%\%\%';
+--------------------+
| 'a%b' like '%\%\%' |
+--------------------+
| 0 |
+--------------------+
1 row in set (0.00 sec)