What, you're using a single regulator to control two inductors? This is insane, at best.
The inductors have independent currents, therefore they must be controlled by independent current error amps.
The only circuitry that can be common is the voltage error amp and the clock generator (which fortunately can help us out by providing a phase sequence, reducing ripple). Well, and any common bias and reference and supply bits.
If you're in discontinuous mode, the currents will track by happy coincidence, only. In continuous mode, both inductor currents are open variables!
Afraid I don't have any insight to the apparent pulse mismatch.
Tim