At 28:29- Alex is wearing ankle boots but at 29:04 they have changed to tennis shoes.
When Booth wakes up in the hospital and checks his phone for missed calls, he redials a call from "Unknown". A blocked caller ID is impossible to redial since no phone number is given.
Liam O'Connor orders his men to triangulate the location of the walkie talkie Alex Parrish is using. While this is possible, it takes coordination between a minimum of three stations with the same frequency and antenna systems oriented to receive the maximum signal strength just to narrow the location down. This means it would be nearly impossible to do on a moving radio and make it very unlikely a veteran FBI agent would bother to order it.
Ryan lying about Alex shooting him can't possibly help her to prove her innocence.