Is it common for panels on a plane's body to not be perfectly aligned?
It looks like you were seeing simple skin lap joints.  Flush skin butt joints are generally used on high speed aircraft, but these joints are more complex to make (you have to use a joining splice strip under the butt joint).  

A lot of the time the manufacturer determines that the local airflow isn't smooth right at the surface (there is a turbulent boundary layer that is maybe 1/8" deep) and a small step in the surface has a negligible effect on drag.  If this is the case, a simple lap joint, that doesn't require the joining splice strip underneath, is used.

There usually isn't a hard 90 degree step on lap joints because it's normal practice to put a fillet of sealant along the edge to make the higher skin taper toward the lower one and this mitigates any drag effects further.