I’ve found the sources of the issue. Firstly, EPEL has errata in its repositories that have packages that exist in other EPEL repos. There was a bug in Katello since 3.16 that caused these cross-repo errata to be excluded from content view versions with filters: Bug #33254: CV Package count ok, but Errata count (huge) mismatches with pulp2 - Katello - Foreman. This is fixed for Katello 4.2
Secondly, I just discovered another bug. EPEL includes source RPMs in its errata in a way that we weren’t expecting. Right now, errata with SRPMs in the package list (more specifically among the filenames) will be excluded from filtered content view versions. I’ve made a note to fix that in the original bug from this thread.