10 speed cassette/derailleur, but only getting 8 clicks? I've got a 2013 Giant Escape 0 Hybrid with a stock 10speed Shimano Deore rear derailleur.  My wife was riding the bike the other day, and somehow managed to shift in such a way that it popped the chain off the rear cassette and jammed in between the sprockets and the spoke protector.  Luckily no damage was done.

After putting the chain back on, I put the bike up on a stand to check/tweak the derailleur alignment.  The small sprocket and the large sprocket are properly aligned.  I can shift up and down with almost no problems; I seem to skip the third gear.

If I take the rear wheel off and click the derailleur, I only count 8 clicks; not 9.

I'm not sure what that means.  Nor am I sure how my derailleur can be properly aligned on the smallest and largest cogs, hit all the shifts except for one, and yet miss an index.

Is this an alignment issue?  Is there a problem with my shifter?  Is my derailleur whacked out of position?  How/why could I be "missing" an index?
If you are skipping gears, I suggest the cable tension need to be reset. Shift to the smallest cog, undo the bolt fastening the derailleur cable and then refasten, ensuring there is just enough tension to hold the cable tight. You should then be able to accurately shift up one gear at a time and go through all 9 clicks. It may take a few attempt to get right, and you should test it with different front gears selected. Also check for worn cable or housings.

Looks like you need to set the limit adjuster also, there are two small Philips head screws that do this. They prevent the derailleur shifting past the largest and smallest sprockets.