Here we go.
Phase issues always come from differences in distance. Reflections can cause them but, technically, that's still distance.
Polarity issues come from one microphone being pushed when the other is pulled, or one microphone being wired in reverse resulting in the same effect,
or one of two speakers being wired in reverse.
It's an of/off thing. Right or wrong.
If your microphones have equal distance from the cab and you know the speakers are wired correctly and you're having an issue, flipping polarity (called phase on your interface) should sort it.
If that's not the case and your issue is comb filtering as a result of the mics being different distances from their speakers, then distance adjustments are your friend.
You could run into phase issues simply because technically each mic has a different source (two speakers), and each picks up the other as bleed, although that shouldn't be an issue if you're very close to the grill.
If you suspect this is the problem, try micing close, or try both mics on one speaker just to see.