We have the "Only backup the Primary" option selected from the 'AlwaysOn Availability Groups' dropdown, as shown in the attached screenshot.
So why are some of our databases still getting backups for the secondary as well as the primary?
That configuration setting does not apply to system databases (such as master, model, etc.) since they are not part of an Availability group. To be eligible to be added to an availability group, a database must be a user database. System databases can’t belong to an availability group.
That those options are enabled for System databases is a LiteSpeed UI defect. This is being tracked as LS-854: "Always on availability group" options ought to be disabled when a user selects “system databases” in a maintenance plan.WORKAROUND
For System Databases, don't select any of the choices from that dropdown. Any option you choose will have no effect.
STATUS
Waiting for fix in a future release of LiteSpeed