When the CCTV of the back alley is shown, you can clearly see its a body double of Delilah and not the real actress that plays that part.
When Tim and Delilah are discussing how Logan used the Cypher to change his grades, Delilah says "Changing his grades? Like Matthew Broderick in WarGames?" Matthew Broderick changed his grades in Ferris Bueller's Day Off.
Kasie said that the deceased had developed a program to by-pass any computer system's security measures. Apart from the fact that this is ludicrous, she called it a 'cipher', which means a code or coding system, not a means to bypass other codes.
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.
Creating a stronger encryption is never a bad idea.
McGee suggests a brute force attack and Casey says "if you want to wait until next Wednesday". Brute force attacks on decent encryption can take decades or more.