When Zoe is leaving with the bad guys Samuel Douglas, played by Matt Servitto, has the bottle of medicine and syringe in his hands. After everyone is gone he picks up the bottle of medicine and syringe again.
When John & Zoe are going through the files, a file is opened before Zoe points to it. When the camera changes the same file is opened again.
When Reese gives the license plate number to Finch on the phone, he represents the letters GHO using, Gray Henry Oscar. The military "phonetic" alphabet for GHO is Golf Hotel Oscar.
When Zoe asks John if he wants to leave the bar with her, he asks her where they're going but his lips don't move behind the wine glass.