My theory on the plot holes
I've been reading some of the comments here and it seems some people are confused by the plot. I admit there's too much left in the open, but here's my theory that seems to fit the "holes" in the plot.
Originally, I believe that JT was killed by Bremmer due to the fact that it was a professional "hit" (one shot to the head, leave a bullet as a sign, etc). It makes sense because Bremmer was on Claudia tail and was just a matter of time until he learned of her whereabouts. Notice that she only took precautions to leave JT after she heard about the contents of the case, so it's reasonable to assume that originally Bremmer would have found out about her relationship with JT and decided to kidnap her in exchange for the documents. JT would still get his blue jacket and green vehicle and would definitely go after her girlfriend to wherever Bremmer instructed. That means he would eventually go to the Buck Naked because Bremmer seems like he was already a regular at the place.
The other "hole" people seem to have a hard time with is how come the case contents changed in the end, but not when the woman and her dog were saved. It's not clear, but it is hinted that Jesse sent a second case after she realized that Carl would kill her father (she was present when Carl got out of the car). The hint for this is when Carl, at the end, says "this is yours" and Jesse offers to pick it up, followed by JT comment that the case was hers all along.
All in all, I enjoyed watching it. It could've been a little more "obvious" at points, instead of leaving the viewer to fill in the gaps, but I think it's still possible to make sense of it. If someone still finds some inconsistency in this, please share.