I think this is similar issue to this:
Solution was at the bottom, try maybe it works:
We ran into the same problem. The root cause was that TagManager wasn’t activated before (and the tables didn’t exist), but with activating not the newest version was applied.
I lowered the version number for TagManager in the DB
update matomo_option set option_value='4.9.1' where option_name='version_TagManager';
and was then able to perform ./console core:update which modified another three tables.
It does seem that the TagManager did not create the tables.