Analog controlled H-Bridge to digitally controlled?
While the FET's are as a H-Bridge, the drive isn't and yes the motor is being directly driven by the PWM

Let me redraw it to be a bit clearer 







simulate this circuit &ndash; Schematic created using CircuitLab

Basically the TOP Ptypes are always held OFF due to their GATE being tied to 12V 

You have PWM going into the gate of the LOWER-RIGHT FET (which will turn it ON). This will pull the RIGHT terminal of the Motor to 0V.

The problem then is the PWM is connected to the midpoint of the LEFT-LEG and thus current from the PWM will flow through the MOTOR down the LOWER-RIGHT FET

Thus your PWM is powering the motor.

How to fix?  remove the connections from the lower GATES to the phase connections. Include another FET to provide as a 5V --> 12V logic conversion. This will allow you to then drive the UPPER FET's.

Connect the FET gates to this FET-buffered PWM







simulate this circuit