I have noticed on a few occasions that entity reference does not interact well with other modules when referencing a taxonomy vocabulary on a node.

Nodequeue's smartqueues do not detect a vocabulary and related terms which have been referenced with entity reference, only taxonomy reference (I realized that this module might be deprecated

Also, when building a "related content" views block with a TID contextual filter to display all the nodes which also have the same taxonomy term as the node being viewed, I find that the block works when I insert a particular TID in the preview, but does not seem to work when I put it in a sidebar region. It is as though the node does not make the TID available for the view to "see."

I noticed that there is a fieldset called "Additional Behaviors" which sounds like it is attempting to address this issue, but, for the Related Nodes construct in Views, it doesn't seem to be working.

Apologies if this has been addressed somewhere else, but I scanned the issue queue for a while and could not find anything related.

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RKopacz created an issue.