As Bernadette, Howard, and Leonard are outside of Raj's apartment to check on him, Howard says he can always feel when Raj is in trouble. Bernadette asks how close the guys were before they got married, to which Leonard replies, "Don't look under that rock." Bernadette had to have already been aware of how close Howard and Raj were before she married Howard, especially after Season 5's The Stag Convergence (2012).
During the recording of 'Fun with Flags' the time on Sheldon's watch can be seen to flip between just after and just before 7pm.
When Raj asks the barista to refill his chai tea, she takes the cup but doesn't take off the cover. She then barely tips the tea container, pretending to put something in the cup.
Raj is seen talking to Lucy without having consumed alcohol. At the start of the episode, they are in a coffee shop and Raj is drinking chai tea.
When Sheldon returns to Penny's door to accept her invitation to attend the play, his 3-knock sequence actually starts off with 4 knocks, then 3, then a final 3.