In the diner, the same rucksack goes past in the same direction outside visible through the window.
They continually refer to having an encryption key and needing to crack it. You don't crack a key. It's a key. It is used to unlock encrypted data or communications. If you have the key you have access to the encrypted data.
The circuit board that was supposedly from the metal detector wand couldn't possibly come from a metal detector. The silk screening says mSATA and the connector on the board appears to be an mSATA connector. mSATA is a small form factor connector for storage, typically solid state storage in a laptop. There would be no reason to have storage in a metal detector.
At time 40:51, the outside of Booth & Brennan's home is shown during their Thanksgiving dinner party. There are no cars parked in the driveway. The next scene shows there are lots of guests in the house that were invited for Thanksgiving dinner.