PWM signal synchronization on Arduino Uno

Hi, everyone
I am a new user of Arduino Uno. I would like to get three PWM signals from pin 3, 5,6, 9,10 and 11. But when I check the waveforms on my scope, I found that PWM waveform of pin 9 is delayed, which means the waveforms for pin 3 and pin 9 are not in synchronization. My frequency for these two pins is 31300Hz , which is the highest frequency. Can anyone give me some suggestions on how to adjust the synchronization of PWM signals with different timers. My application is half bridge converter. If two signals are high at the same time, there will be short circuit.The attached is the mismatch of two waveforms.
Thanks in advance.

The underlying hardware is capable of doing what you want. However the Arduino analogWrite() function is not.

You may be able to simply change a few of the timers and reset them to zero simultaneously but I suspect that this project will send you back to re-read the datasheet a hundred times before it's finished.