I tried creating a separate module for all my subscription definitions, and all of the subscriptions broke that were using the entities macro. The compiler spit out some undeclared variable warnings, but other than that, there was nothing useful for me to debug it. Replacing usages of entities with entity at least got rid of those warnings, but it took moving everything back into the same module for the usages entities to work again.
The subscriptions are nothing fancy either, so I have no idea what the issue was. Here's an example:
(defsub :notes
[?eids <- (acc/by-fact-id :e) :from [:note/creation-date]]
[(<- ?notes (entities ?eids))]
=>
{:notes ?notes})