After Dipper, Mabel, Wendy, and her friends enter the van, Tambry is nowhere to be seen in the van as they are driving.
When Wendy, Dipper, and Mabel are throwing pine cones from the roof of the mystery shack, Dipper throws one at a van. Moments later Wendy's friends show up in their van Right next to the other van. In the next shot the other van has vanished.
When Wendy reveals the passage up to the Mystery Shack's roof, it has a wooden door covering it. But in the next shot of it, it is an open passage through the ceiling.
As the gang are waiting for Dipper to scale the fence, Lee is already on the other side. However, Lee is then seen climbing on top of the fence from Dipper's side to throw him off.
When Wendy congratulates DIpper for hitting a van with a pine cone and setting off its alarm, she offers a high-five with her right hand. He uses his right hand to complete the high-five. But the close-up shot of their hands hitting, it's her right hand and his left (the thumbs are in the same direction). Then cutting back, he's withdrawing his right hand.
When the ghost at the convenience store levitates Dipper, he looks down and sees his shadow on the floor shrinking. But in reality, if an object gets closer to a light source, the shadow cast from that object based on that light source should get bigger.
When Wendy, Dipper, and Mabel are throwing pine cones off the roof of the Mystery Shack, Wendy offers Dipper a high-five after his throw. However, she and Dipper only have four fingers on their hands.