If you are using Half-Bridges – CONTROLLINO MEGA, there is internally freewheeling diode because of low side transistor internal body diode – no need to connect it externally.
The problem is probably following. Because your motor is turning ON on the full speed, and you want to switch it OFF, you set both low side transistors to short circuit and motor is for the short time working as a generator and it generates such high current, that is detected as over-current inside the CONTROLLINO and reported as overload. This functionality with both transistors to low side is used for hard brake of the motor.
If you don’t need the hard brake, switch it OFF in the way that for short time you switch OFF only the high side transistor and then ON the low side (play with proper timing in your application).