The motan step_phase is intended to show a statistic similar to mscnt, but with a few notable differences. The step_phase increments between 0 - (microsteps*4-1) (whereas mscnt increments between 0 - 1023). The step_phase should always increment while the nominal stepper position increments (whereas mscnt may increment or decrement depending on the dir_pin polarity).
The two values don’t necessarily match, but it does seem like something went wrong with the values that you are reporting.