On latest internal build I get
— source
CREATE TABLE `t1` (
`id` INT(11) DEFAULT NULL
) ENGINE=INNODB DEFAULT CHARSET=utf8 COMMENT='this';
— target
CREATE TABLE `t1` (
`id` INT(11) DEFAULT NULL
) ENGINE=INNODB DEFAULT CHARSET=utf8 COMMENT='that';
— ALTER script
ALTER TABLE `t1` COMMENT='this'; — no comma
So either this requires a specific table to reproduce or it has been fixed in between. I will discuss with team tomorrow.