Not sure what you mean, you have to use opposite phases on a 2 wire shared neutral circuit.
Are you using a 2 pole AFCI breaker?
I believe a 2 pole AFCI breaker will solve your problem because you will not have to create a 3 way splice in the panel for the 3 wire neutral to be connected to both single pole AFCI's.
What I think is the 2 single pole breakers are reading the neutral current and it's not matching the current draw in your ungrounded conductors.
That's correct, and the neutral would have the difference, 3 amps on it.Let's say you've got 5 amps drawing on one breaker and 2 amps on the other, the current on the neutral will not be the same , because the neutral I carrying the current from both circuits and will not match on either breaker the unbalance should trip the breakers just like they would if they were GFCI breakers.