It is stated that the stabbings were made with a 6" long, single edge, serrated knife. In some of the flashbacks, the killer is shown stabbing with a double, straight edged knife.
The biker is supposed to be loosening the lug nuts on the prison van but is shown turning them clockwise. This would tighten them.
When Frank and Caine talk about evidence found on a Boston murder they mention Redfish scales were found. Caine then mentions mosquito lagoon is the only place in the area to find redfish. Mosquito lagoon is not located anywhere near Miami in fact it is located around 300 miles north. Also while mosquito lagoon has a large population of redfish it is not the only place in Florida they can be found.
The second victim's Y cut-pattern signature is shown to be fake because a portion of the Y shaped scab is raised above the skin and the skin below it is unharmed.
In the flashback of the biker loosening the wheel nuts on the police van, the suspect uses a tire iron but the sound is that of a ratchet type socket wrench
Loosening the lug nuts on the van, would have caused severe shaking, especially for the amount of wobble that was shown. The occupants would not have been seen riding smoothly and would have called for a maintenance van, long before getting up to the speed that would cause the van to flip and kill the driver.
Why is Horatio standing on top of a skyscraper at the end of the episode? Sure it is a cool looking shot, but there is nothing in this episode, or in the character's history to explain why he needs to go to the top of this particular sky scraper to reflect on things that bother him.