I hit this with Wikidata, but later (T185114) it stopped working entirely: https://phabricator.wikimedia.org/diffusion/EWBA/browse/master/lib/includes/Store/Sql/WikiPageEntityRevisionLookup.php;f37e244cd624ead83bc9552ff0b5d4c23880948e$199 .
Originally, all the Vagrant wikis shared the same external store: https://phabricator.wikimedia.org/source/mediawiki-vagrant/browse/master/puppet/modules/role/templates/externalstore/conf.php.erb , unlike production.
Background: In production, each wiki (e.g. enwiki) has corresponding enwiki External Store databases, but they are not the same database. There may be more than one blob table in this other enwiki DB (e.g. blobs_cluster1, blobs_cluster2) (I'm not sure if having multiple blobs tables in the same DB happens in practice in production), but there are no non-blobs tables.
As a temporary solution on Vagrant (T185114), we will put the blobs tables in the main DB (where the other tables are) on Vagrant without changing users. But this makes it potentially possible for code to falsely work locally (by accessing a table that should be elsewhere).
To solve that, we should either restrict the tables by user, or setup a whole separate MySQL (AFAIK this is the only way to have two databases with the same name on one computer).