In "The Agreement Dissection", Sheldon says to Leonard that he hates Greek food and Leonard answers "Not as much as you" which is a confusion quote because it refers to 2 phrases: "Not as much as I hate you" and "Not as much as you do".
In "The Intimacy Acceleration" Penny discovers it is Sheldon’s birthday. She responds with “I never took you for a Pisces”. This contradicts the episode in season 1 “the peanut reaction” where after an argument between Sheldon and Penny she says “you are a typical Taurus”.
In "The Maternal Combustion", Amy was absent during the visit of Leonard and Sheldon's mothers Beverly Hofstadter and Mary Cooper. This was because her portrayer Mayim Bialik had to take some time off to be with her family following her father's death that had happened recently. The plot hole here is that since she is absent, it is unexplained and unknown where she is and why she could not be there and Mary doesn't even ask Sheldon about her and Amy doesn't even tell Leonard, Sheldon and Penny why she can't be there during the visit of the mothers. Also Beverly asksLeonard, where Mary is from and after Leonard answers "East Texas" Beverly is annoyed, this is at first a plot hole because she should know where Sheldon is from since they know each other really good, also she actually likes Sheldon who is also from Texas.