Plot hole: In the episode "Lows in The Mid-Eighties" during the flashback scenes, it is shown to us that Will comes out of the closet during his freshmen year of college during Thanksgiving Break, when they spend the weekend at Grace's Parents house. However in the episode "Willian, tell" Grace claims that Will came out to her at senior year of college during Christmas Break. Quite a difference for such a memorable time.
Revealing mistake: After the opening credits there is a shot showing the house on the island where Karen and Stan live. If you look at the hanging chair, you can see that Karen is sitting in it. But in the very next shot she is in a meeting with Will, in a different outfit. This is a re-used shot from the previous season, which shouldn't be there.
Continuity mistake: When Grace is telling Will about his dad's affair, she mentions that he grabbed the other woman's ass when she brought him a packet of Goobers during the interval. The thing is, she sees them for the first time during the interval, and we see the conversation that follows. The mistress brings him wine, not Goobers, and he doesn't grab her ass.
Plot hole: The apartment block where Will lives supposedly has the same layout for each floor of the building. Yet in "Yours, Mine or Ours" the room 12D is seen as located right in front of the elevator, the same location as Will's apartment door - however Will's apartment is always seen as 9C.