I am noticing a number of bugs / errors with Orion Maps and the automatic topology creation. I have several devices that do not communicate with each other being automatically mapped as if they are connected. The whole point of the map, is to view the topology for all 3 sites on 1 map, so I will not be turning off the "topology connections". See below diagram for reference.

Each router (Cisco 4451-X) has a switch module (Cisco SM-X-ES3D-48-P) embedded within, reachable by a backplane interface. Interface Ethernet-Internal1/0/0 interface on the router, and GigabitEthernet0/52 on the switch module. Router A connects to Switch module A, Router B to B, and C to C. These are the only connections that should be present, as these routers and switches are all in geographically separated regions, AND they have no way to communicate to each other.
Issue 1:
Between Router A and Switch Module A, it automatically mapped 2 different connections, with only 1 of them being correct. It mapped:
Ethernet-Internal1/0/0 to GigabitEthernet0/52 (correct)
BDI1 to GigabitEthernet0/52 (incorrect).
The BDI is a virtual interface, and it thinks it connects to a physical interface (Gig0/52). BD1 would connect to VLAN 1 on the switch (although this is shutdown). The other odd thing is that the other BDI's aren't mapped the same incorrect way. I have a dozen or so other BDI's that it should pick up for the same consistant (but incorrect) way but they don't.
This same exact issue, is present on Router C to Switch Module C with the same corresponding interfaces.
The same issue between Router C and Switch Module B is present, except that there should not be a connection between them.
Router B to Switch Module C only has the E-I1/0/0 to G0/52 automatic connection (instead of the BDI one as well), but that too, doesn't exist.
Issue 2:
Switch Module A's connection to Switch Module C doesn't exist. It sees this connection as follows:
SM-A GigabitEthernet0/52 to SM-C VLAN 20
Somehow, it's mapping a physical interface at 1 geographical location, to a VLAN on a different switch blade (which again, doesn't exist) at another location.
Issue 3:
Router B to Switch Module B should have the E-I1/0/0 to G0/52 connection mapped, but it doesn't find it automatically.
Issue 4:
Not pictured, but similar to the first issue. I have another router connected to a switch with 2 physical connections over a port-channel. The connection seen is as follows:
Router port-channel 11.22 to Switch port-channel 11. Somehow it mapped a subinterface (11.22) to a port-channel instead of mapping it to VLAN 11.
All of these routers and switches are configured exactly the same (with only the IPs' 3 octet changing per location) with the same interfaces and names connecting to each of their respective switch modules, but each side has something different automatically created. All of the interfaces on all devices that are checked to be monitored on each node are the same. It is odd that even the incorrect connections don't seem to be consistent throughout.
I hope this helps to correct the issue. As a solution for me personally, I want the ability to delete (or turn off) the automatically generated links so that I can do them manually. I would stick with Atlas Maps, however the upgrade to 2020.2.5 killed one of my maps (it no longer shows status colors on objects). I'm assuming that is part of the "deprecation" of network atlas that is mentioned in the patch notes. This doesn't fix the underlying issue, but it is a work around that fixes my problem.
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