Kasie says (of Prof. Harding's behaviour) "It's also pretty strange. It's not like him." However, she joined NCIS as an outsider, a scientist, not an agent. She would not have come across him because she didn't attend FLETC training, so she would have had no idea what he was like.
Kasey points out that a lot of the files on the dead man's computer start with N.S.S.C.I. You wouldn't use all those periods in a file name.
Casey and McGee state they are monitoring the county sheriff's communications, but the software-defined radio they are using shows not only an HF frequency (not likely to be used by a sheriff's office), but it also shows the mode is RTTY, which is a data mode not voice.
Vance states that the DOD didn't know that information was missing from their servers, to which Parker says "So, it was stolen." This is the same misconception (revealing computer illiteracy on the part of the scriptwriters) seen a previous episode, i.e., that stealing computer data is like burglary. In fact, if you steal data from a computer system, you are merely copying it and it will still be there, unless you deliberately delete it. That would be stupid, because it would show that the system had been hacked.
After reading the contents of a 3½" floppy disk, Kasie splits it open and finds a folded-up photograph, three layers thick, with a printed message on the reverse, fastened inside. There is very little space inside one of those disks, so, if that message had been in there, the magnetic disk inside would not have been able to spin and the disk would have been unreadable.
After learning (in spite of lack of cooperation from the Deputies) that a Sheriff's Department squad car 117 is missing, Kasie immediately has the car's GPS locator on her computer. It is highly unlikely that she would have access to that information. Even if she some how did, it would take a while to call up the information and lock onto the car in question.
It is understandable that Prof. Harding kept a scrapbook about his former students. However, opposite a press clipping about Torres, there is what appears to be the original of Torres' FLETC graduation certificate. The Professor could conceivably have a scan or photocopy but not the original.
McGee phoned asking the sheriff for road blocks to be set up, but Casey already has the professor's phone from the "unknown shooter". If the phone could get to Casey, the shooter would be well away from the area of the shooting by that time.