I have had this happen a couple times with my driver side window now.
When I roll it down I hear a thud sound, then I realize it rolled down about 1/4 inch lower than normal. Normally it rolls down where there is just a fraction of glass above the window guard or whatever it is at the top of the door, but 2 times now the window has rolled down past this. If I roll it up some then back down it goes to the normal position.

Anyone else have this happen, and can you think of anything its harming?

 

sounds like your window track or track stop, may be loose
Take it in and let them adjust and tighten. One day that glass will jam or get off track. You don't want that to happen! Power windows usually end up, not going up or comes crashing down on either front or rear of glass. Learned my licks with windows, working for a dealer many year ago, doing factory claim work like yours.
Fix it! It won't fix its self!
Happy Trails!!!

 

Try calibrating it.
Manual tells you how.

 

I'm with Ponyboy66... it is in the manual...

 

Same thing has happened to me a few times now as well. Recalibrating I'd say is not the answer because when I hear the thud and see the window is down a bit, I can roll it up a little and then back down and it stops in the correct place and works fine for several weeks and then all of a sudden I hear the "Thud" again. I have recalibrated several times because the good ol' comp forgets how to auto roll up the windows.