The writers have obviously confused an iris scan with a retinal scan.
Casey says the file shows Sokolov defected in 1985. However, Duckie remembers it as after the fall of the Berlin Wall, which was in 1989.
Jimmy said that he could only give a very rough estimate of time of death based on rigor mortis and couldn't do better until he got the body back to the autopsy room. However, it is standard procedure (often used in the show) to take liver temperature of the body in situ, and this gives a much more accurate and precise time than rigor.
Jimmy says the time of death was "30 hours ago" and Torres says that would be "about 6:30 last night". That would make it about 12:30am. However, Jimmy's daughter is waiting for help with a school project and they expect Parker to be having dinner with a friend, which would make it early evening.
When Parker is in the interrogation room with the Senator he points out the CCTV camera. The camera should be flashing red to signify it is recording but there is no red light to be seen.
The team members come back to the squad saying that they have been unable to find anything about Evelyn Shaw and the various agent swap deals. Jimmy says "Same here" but finding intelligence like that is not even remotely part of his job as a medical examiner.
It is not possible to get a usable retinal image from a high resolution photograph, even a 8K UHD photo, if that were possible it would render biometric retinal scanners useless. Retinal scanners that are part of a biometric security system use a low energy infrared beam of light to obtain an image of the blood vessels in the retina, the pattern of blood vessels for a person are as unique as fingerprints. Regular photographs are taken with visible light, it would not be possible to get an image of the retinal blood vessels from a normal photograph. Even if someone took a IR photo of a person they would need to have the camera lens directly in front of the eye to get a usable image.
Knight and Torres get a ride on a supply chopper to the USS Cortland. The Cortland had just left harbour so it should have no need for a supply chopper, unless the admin staff were sloppy and forgot something. It also seems a bit small to be a supply chopper (although the ship's helipad couldn't have taken anything bigger). Vance said the chopper had room for only two agents. Although it was too small to have been a freight helicopter, it was certainly big enough for more than two passengers. (To be fair, the job didn't need more than two.)
The hard copy of a top secret file is missing. McGee is able to identify it from a digital archive and Kasie later shows an image of its cover on-screen. It seems odd that there is only one copy of such an important file and that whoever took the trouble to scan the cover didn't scan the whole file.