When Kevin is shown the note, it is intact. The processing flashback clearly shows significant holes being punched out for ink samples.
Caine calls the .22 Long Rifle bullet recovered from the body suited for long distance shooting. It is not. The bullet is pure lead and not strong enough for the high muzzle velocity required to make a long distance shoot.
When they bring up information from a suspect's fingerprint and see that it is a GS-14 federal employee, they assume that the GS-14 is the suspect's government security clearance. GS-14 is a pay grade in the federal government, and has nothing to do with the level of a government employee's security clearance.
When using chromatography to prove the year the ink from the note was made, there needs to be a reference to compare the sample against. Otherwise, the bands are meaningless.
When showing Luis the "proof" his gun killed Bob, he is shown a picture of the muzzle stamp on Bob's chest alongside a picture of his pistol's muzzle. The problem is, on the body, the diagonal line defect is moving barrel down to the left from the perspective of the shooter. But on the pistol, the diagonal defect is barrel down to the left from the perspective of the victim.