A few comments and questions:

Calls actively ringing to an extension will take priority over calls which have already been answered and placed on hold.

You stated line appearances and call appearances. Which is it?

What does the display show when the calls are being presented?

Are you positive that these are hunt group calls? Could this be an attendant station or otherwise receiving recalls from another station or hunt group?

Is it an ACD hunt group? If so, what happens when the agent is logged out?

If these are indeed ACD calls, and Wrap Up Mode For Holding ACD Calls is enabled, you should never see multiple calls presented to any agent.

There’s definitely a piece of the puzzle missing.