When John is robbing the jewelry store, he shoots David once. When the team is investigating the robbery, Stottlemeyer says that David was shot twice.
The scarf given to Mr. Monk by Marge, supposedly hand-made, has a label attached.
Investigating a suspect, Captain Stottlemeyer walks into an open garage, lifts a tarpaulin, and finds key evidence under it. Under the "Horton test," unless police have a search warrant, they can only take note of evidence "in plain view." Under a tarp is not "in plain view." so the evidence would have been excluded as a violation of the Fourth Amendment. There was no mention that a search warrant had been obtained.
In the opening, the guard falls over the railing, and is then shown as impaled on the swordfish, but the angles are all wrong. Falling down, the guard may have been injured but he would have knocked over the display instead being run through.