I had the same problem (update from version 4.13.3 to 5.0.3). And a ./console core:update indicated that everything was up to date.
But in the “matomo_tagmanager_container” table, the ignoreGtmDataLayer field was missing.
I manually modified my table:
ALTER TABLE matomo_tagmanager_container ADD ignoreGtmDataLayer tinyint DEFAULT 0 NOT NULL;
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.