Leonard notes that he and Penny haven't spent time alone together since they broke up, though they spent an evening painting each others nails and reminiscing in The Staircase Implementation (2010). And they also had sex after she and Zak broke up in The Lunar Excitation (2010).
When Sheldon puts the bird's water cup on the end table, a red blotch on the cup faces the camera. The cup rotates by itself to a blotch-free side between shots. Also, the cup disappears completely when the bird flies out the window.
When Leonard and Penny are at the movie theater discussing which movie to see, the extras in the background walk by twice in quick succession as the camera cuts to Penny and back to Leonard. It is clearly two different takes.
When Bernadette takes the photo of Sheldon and his bird, the bird looks to the left (on the phone's screen, you can clearly see when the photo is being taken). On the posters in the staircase, the bird faces the camera almost directly. According to the bird's viewing direction, the photo must have been taken about two seconds later.
Sheldon refers to the bird as a blue jay, however, it is a black-throated magpie-jay.