with some ships if i try to get it to autopilot a manuver it will work fine until the burn starts and then it just starts turning throttle on and off super fast.

i made sure that the COM was completly balanced and it doesnt wobble or turn when i manually use throttle. it seems like it happens more on big ships. i turned off all the options in Utillity in case they were causing problem and same thing happens

that fixed it thanks!

Make sure you have a control point set on your vessel. Select "Control from Here" on the command module or drone core.