In "Runners" we learned MacGyver was seven years old when his father died, but here he claims to have seen him when he was ten years old.
Despite the fact he's working undercover to infiltrate the logging company, MacGyver uses his real name.
A photo of crumpled, burnt paper shows it to be perfectly flat.
The police interrogate Roxy, a primary suspect in Rogan's death. However, she produces an alibi so iron-clad that they don't at all believe she was responsible. It's implied there were witnesses at her workout. And yet as the episode proceeds, it's clear that her alibi was false. How she was able to create an unbreakable false alibi is overlooked for the rest of the episode.
Deegan has an operator trace an "open line", but since Pete hung up the phone, this would not be possible.