Slight differences in motor Kv. (they are typically manufactured with a +/- 10% or +/-5% tolerance)
Differences in PWM (“PPM”) pulsewidths. Are you using PPM? Tune it so the control goes from -105% to +105% as you physically operate the throttle control from one end of its range to the other. If one motor is stronger at top speed, set that one to -107% to +107% instead and keep the other side -105% to +105%.
Also OMG use the desktop application LoL 
You crazy