FindIT does not explicitly support the Meraki portfolio, so the access points will be identified based on how they advertise themselves through LLDP/CDP. I must admit I'm not all that familiar with the details of the individual Meraki and what you can and can't configure on them and I don't have any available in my lab, but my first step would be to make sure that both the APs and the switch they are connected to have the same discovery protocols enabled. Then look on the switch and see exactly how the APs are advertising themselves.
As for the extra connections in the topology, that could certainly be due to mesh. Depending on what protocols are being forwarded across the mesh, we could be seeing two switches appear to be directly connected when in fact there is a mesh network between them. To get to the bottom of this we would need to look at the specifics of the network topology and what FindIT is displaying. It would be a good start to open a case with the support team, so an engineer can work with you directly to collect the right information. Have a look at https://www.cisco.com/go/sbsc to find the local phone number in your area to access support.
Cheers,
Dave.
