Most swimming problems like you're describing are caused by water quality issues, so yes it could well be from a level of ammonia higher than 0, or overfeeding (which can cause an ammonia or nitrite spike in the tank) Best way to deal with it is to euthenize the fish that is affected and step up your water changes and maintenance on the tank. You should be changing about 35% of the water once a week and doing gravel vacs....more if the tank is less than a couple months old and still cycling.