Ok, no that it is clear you are using normal brushed motors, I think I can explain what you are seeing:
A motor can be seen as a series connection of an inductor (the winding), a resistor (copper resistance of the winding) and a voltage source (back emf).
The inductance and the resistance form a time constant. As long as the PWM frequency is higher than this time constant, the current is more or less constant (there is a bit of ripple, but the current does not go to zero between the PWM pulses). For typical motors this time constant is in the range of 1ms. That's why the PWM frequency of typical motor drivers is in the single digit or lower 2 digit kHz range.
Going higher reduces the ripple, but also increases switching losses and also losses in the iron core of the motor. Sometimes >15kHz are necessary if you need to be outside of the audibility limits.
If you go below 1kHz, the ripple current increases. In your case you have both a low and high side switch in the half bridge, meaning the motor is connected to either the supply voltage or shorted. With a low PWM frequency the current ripple gets so high, the direction of the current actually reverses when the motor is shorted by the low side switch. So the motor accelerates and deccelerates at the PWM frequency. The high peak currents because of the acceleration and decceleration generate a much higher rms current therefore everything gets much warmer than at a couple of kHz.