Just as Sheldon is about to enter their apartment, Leonard knocks on Penny's door. Sheldon says, "Penny" but apologizes after Leonard looks at him. WIth Sheldon having issues about closure, he would have made a fuss about not being able to complete the 3-knock cycle. No, he wouldn't. In the last episode he showed genuine compassion towards Leonard and he does have the capacity to pick up on other's emotions.
Raj didn't seem to recognize Bert in Amy's lab. This is the second time they have met. The first time was in S6E18 The Contractual Obligation Implementation (2013), when Raj was setting up his texting date with Lucy in the library, Bert sits down and they have an awkward exchange. Bert gets up runs into Lucy on his way out and tells her, "You can do better," before exiting the room.