It's normal for the freewheel to be a little bit off and not perfectly concentric with the axle. If it's off center and you removed the cones, you might have reassembled it with the spacers and washers in the wrong position or forgot to put some of them back on. If you switched cones to new cones, they might not have the same dimensions. A more unlikely possibility is you put too many balls on one side but this would make it harder to put back into the frame.