Replacing too much water during a cleaning is bad for the fish, even though you may have put the water conditioner in the new water. I've heard different takes on how much you should take out, but its almost always around 25%
Also, you need to match the temperature of the new water with the old water. Put in water thats too hot or cold will shock the fish.
Fish are very susceptible to stress. Doing things in moderation will reduce harmful stress.