Smart chargers, like smart people are often dumb and get it wrong.
The slow charge is only to stop a quick overload, leaving it on all night can create a slow overload.
The issue is more to do with the smart Power Control Chip than the charger. The PC Chip may continue to charge the battery. It communicates with the charger if it can, to decide what voltage to request dependent upon battery voltage.
It could be that the Qualcomm chip isn’t working optimally, ask Fairphone if that could be the case.