Yes it could definitely cause a problem. A 48 Volt battery charger should be used with a 48 Volt battery pack. I recommend buying a 48 volt charger. Otherwise the battery pack will overcharge which will cause it to wear out and fail prematurely. Charging a 48 Volt pack with a 60 Volt charger could also damage the charger because the battery pack may never reach 60 Volts and the charger would not turn off which could cause it to overheat.
When installing new batteries for our Zapino, we damaged the terminals of one battery. We're running 48V instead of 60, and the power and speed seem just fine. Our older lower-amp charger worked for a while since the change, then stopped. I'm getting a new Zapino 60V charger. Will this be a problem if only charging 48V?