While on the docks when Hook is talking to Smee about taking Henry to New York on a boat just before the flying monkey attacks them, it is snowing and the ground is covered. Later, near the end when Henry and Emma are talking by Neal's grave, there is no sign of snow anywhere and it looks to be fall instead of winter.
Aurora is pregnant when everyone comes back to the Enchanted Forest, but when Snow is planning announcing to her pregnancy (conceived after Aurora) Aurora still does not show.
When Snow and Charming are going to announce their pregnancy she is already seemingly several months pregnant, yet in the next scene it says 8 months later.
During a flashback from the missing year, when Prince Charming, Snow White, and Regina are in the forest looking for something that could lead them to Glinda the Good Witch (eventually finding a door), Charming picks up a flower for Snow that happened to be related to her name's origin. Snow takes it and in a following conversation with Regina, calls the plants "snowbells". In actuality, snowdrops are among the few plants that can survive the harshest winter (how Snow got her name); the flowers are called snowdrops, not snowbells.
When Zelena freezes Snow and Charming you can see Ginnifer Goodwin blink several times when she was supposed to be frozen. However, the show and spin-off show numerous times that this is normal and people can still move their eyes when magically immobilized.
When Snow and Charming go to see Glinda, only the pure of heart can visit her, but Snow's heart was blackened after killing Cora. However, just as they can blacken, hearts can also become pure again.
When standing at the dock, Colin O'Donoghue's natural Irish accent slips through when insisting someone sent him the message for Emma.
When the Wicked Witch kidnaps Hook, he says that she didn't need to as they were in Storybooke and she could have used a telephone. Later in season 4 he pulls out a cell phone to call Emma and doesn't know the name of it to tell Elsa.