After some investigating, this was caused due to partial shared neutrals on two 3-way lighting circuits - instead of wiring with proper 3 wire cables between the switches, they used 2 wire cables with the white used as the traveler. This caused them not to have a neutral at the light fixture, so they just pulled the closest cable.

In one instance they re-used a neutral from a different circuit that was in the 2-gang box, and in the other the pulled a 14/2 wire and only used the white wire (leaving the black wire simply cut off).

These shared neutrals basically tied all 3 circuits together, making AFCIs impossible to use without fixing the crossovers.

Temporarily disconnecting the neutral crossovers allowed the AFCI breakers to work, and I will be redoing the 3-way wiring completely to have a permanent fix.

After some investigating, this was caused due to partial shared neutrals on two 3-way lighting circuits - instead of wiring with proper 3 wire cables between the switches, they used 2 wire cables with the white used as the traveler. This caused them not to have a neutral at the light fixture, so they just pulled the closest cable.

In one instance they re-used a neutral from a different circuit that was in the 2-gang box, and in the other the pulled a 14/2 wire and only used the white wire (leaving the black wire simply cut off).

These shared neutrals basically tied all 3 circuits together, making AFCIs impossible to use without fixing the crossovers.

Redoing the 3-way wiring completely has solved the AFCI trips and kept the 3-way switches fully functional.