Be very careful when using the ALIGN command if your destination points contain varying elevations (Z values).  The ALIGN command is a 3D command!  If your destination points vary only slightly you won’t see the distortion but when you list your results, it will have a “Extrusion direction relative to UCS:”

You can work around the problem with point filters.  When prompted for destination points, enter .XY, then use your object snap, then CAD will prompt for a Z, enter 0.0.  This way you will get the alignment without the extrusion problem.