Plot hole: Joy and Sadness are stuck outside of the control center. They are trying to figure out how to get back, and encounter maintenance workers who are discarding old memories. The maintenance workers show that they have the power to send memories back up to the control center to be played. Why couldn't they send the core memories that Joy had back up the same way? Better yet, why not use that method to send Joy and Sadness back up to the control center? The director of the film is even aware of the plot hole, and said "Yeah, well then we wouldn't have a third act," before explaining how the idea of recalling memories was added in later, "box[ing] [the screenwriters] in a corner a little bit."
Plot hole: During the scene where Merida gives her speech on "breaking tradition", her mother, as a bear, moves silently behind the majority of the crowd, so they don't see her. Fair enough. However, Merida and her father's clan are all looking in the same general direction (towards the crowd) while she's speaking - how does no one from Merida's clan see a bear moving at the back of the room?
Plot hole: The first night the toys spent in the Daycare, when Buzz finds Lotso's band playing in the vending machine, there are no trucks patrolling the hallways, and the monkey does not sound the alarm when he sees that Buzz escaped. However, when Woody comes back later, he finds out that those security measures operate every single night.
Plot hole: At the end when the gang get home to Andy's room, it's night time and the luggage trolley they drove home in is outside the neighbour's house. The next morning it's still there. But we see an ad with the 'chicken man' looking very sad because he lost Woody and the others. How could he have gone to Tokyo, realised the dolls were missing, then zoomed back to Tri County to do the ad the next day? While saving Woody, the toys explicitly say that Andy is returning home the following morning. They must have made it in one night, or they would have missed Andy's return.
Plot hole: The first team that gets eliminated in the scare games cheats but Dean Hardscrabble hardly seems to care. Oozma Kappa cheats and she has all of them expelled.
Plot hole: When Sully and Mike are talking in the toilets, during Boo and Sully's Hide and Seek game, Boo comes running in screaming and upset because she's just seen Randall, and he's not too far behind since all three can hear him talking offscreen to the CDA before entering the toilets, but how did Boo get to Sully faster than Randall without him seeing her, and how did Randall not hear her screams since they're all in the changing rooms which have an echo?