Hi @TechBoii, welcome to the forum 
Sorry to hear you’re having issues with your Blue Robotics products.
The thrusters do not have influence over when they run, so this is most likely an issue with the PWM signal being provided to the ESCs (by the autopilot), or with the ESCs themselves.
If you’ve confirmed this to be the case then the most likely cause is an ESC issue. I’d suggest reading this thread for some context / ideas, and steps on what to do next (which in this case is most likely contacting our support email).