Presently when updating a mediawiki that takes part in a wikifarm which partially shared table (interwiki, users, etc.) to a new version, update.php not only updates the tables from the wiki it is run on, but also the database schemata of referenced in wgSharedTables.
We do disable wgSharedTables when testing and reenable it afterwards, but it is a constant source of potential errors. Usually the earlier versions which rely on the earlier schema break, whereas some care has been taken to make later versions run with (at least some) shared tables of earlier versions. For example, this is presently so with users in 1.18, 1.19, 1.20.
I wonder whether it would be relatively simple to exempt the tables listed in wgSharedTables from being affected by update.php. If so this would remove one headache from testing new versions or having a mixed-version deployment (at least for a while).