During the shoot out at the end, Reacher is dismayed to find himself armed with a knife. This is a possible reference to the book "Nothing to Lose", in which Reacher claims to hate using a knife in combat as he has "no particular talent for it".
The "highway bridge" the sniper should have used is the I-279 bridge. It is shown to have the sun behind it (west) in both the original shooting and the hypothetical discussions. This would mean it's evening (sun is low in the sky, during summertime) - not the morning, as indicated by the shooter's watch and the victims' stories.
Jack Reacher: [after killing Charlie in a brutal hand-to-hand fight, Reacher confronts Emerson, who is using Helen as a human shield]
I know you're in there, Emerson. It was staring me right in the face. The one piece that just didn't fit. The quarter. Nobody would have thought to dump that meter. Not even me.