Bartek,
I think you are going to have to give us more information as we are only guessing, trying to read between the lines.
I think you need to give us a sketch of system with all components.

Water temperatures in/out heat exchangers or air on/off.

If you are using water through a heat exchanger then there is possibility of spot freezing, especially if water flow is down & below zero. Normally flows switch or evaporator pressure regulator.

A few other temperature readings along suction line would be helpful to determine flood back is occurring. if superheat immediately out of evaporator is example 5 degC at evaporator outlet,
what is it at compressor? is there anything else in the suction line.

Maybe discharge & sump temps when running"normal" compared to "flood back " condition.