Get Bad Link Detected alarms for switch ports that are configured not to trap on link status. The "Connected Devices" appear to be IP Phones (the MAC addresses are consistent), or some other device, and these connected devices are not SNMP devices and they do not show up on the topology view. When this occurs, they are on Physical_Port models connected to switches.
The cause is that the links have a Physical_Addr model. If Create Physical Address option is enabled, discovery may create Physical_Addr models to represent non-intelligent devices (IP phones, and so forth) that were heard by the switch ports. A connection will be created between the Physical_Addr models and switch ports. To address this, use Locator to search for all Physical_Addr models and destroy them. If there are a large number of them, select and destroy in a few chunks until the entire population of these types of models is gone. Removal of these should have no consequence (the option to create is turned off by default).