Sitting at a table on his patio, SECDEF drinks from a glass of water, to wash down his pills. In the previous shots, there were no glasses on the table, only cutlery (flatware), cups, saucers, plates and napkins.
At an international function such as the event at the SecDef's home, there would be an actual armed security detail at the gate, not just a stuffy aide standing in the driveway.
Gibbs has only recently adopted the wounded dog, Lucy, but when he goes to answer the door, he commands her "Stay." He has not had enough time to train the dog to obey his commands. She was previously a fighting dog, normally kept in a cage, so "stay" was presumably not part of its vocabulary.
Correction: A presumption is not a fact. There's no reason a fighting dog couldn't be trained not to run riot every time it was let out of its cage.
There is also no exact timeline given, so Gibbs could have had the dog for a few weeks by this time. "Stay" is a fairly simple command to teach, and can be taught in a few days, with enough work, and a reasonably smart dog.
When Bishop and Nick arrive at the piano player's apartment, they knock and identify themselves. Agent Sawyer, just inside the door, should've responded immediately, instead of remaining silent, dropping the plate, and providing probable cause for the forcible entry.