As a rule, I never select "Get Interfaces with Topology" unless it is a brand new firewall install and I'm positive that the routing table of the firewall is correct. Even then I still look it over carefully afterwards, and I even warn about this situation in my book although it is not directly performance-related. In my opinion once a firewall is in production, one should always select "Get Interfaces" from that point on and manually configure antispoofing for any new interfaces, as the consequences of an improper topology calculation can be so dire as you regrettably discovered. Hopefully you know about this downtime-free trick I covered in my CPX presentation to disable firewall antispoofing on the fly if it is cut off from the SMS:
fw ctl set int fw_antispoofing_enabled 0
sim feature anti_spoofing off; fwaccel off; fwaccel on
Now that I've climbed off my soapbox, in your specific situation do the two interfaces involved have a relatively long interface name or are subinterfaces with a long VLAN tag appended? I'm wondering if perhaps the topology calculation has some kind of length limit for interface names. So for example if the limit was (a purely hypothetical) 9 characters, it would confuse the first two interfaces in this list but the third one would be fine:
eth12.1001
eth12.1007
eth12.1011
Only other thing I could possibly think of is some kind of VLSM or subnet overlap between the routes associated with the two interfaces? Perhaps if you could post the ifconfig and routing details of the two interfaces it intermingled (redacted as needed of course) that might help.
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