Velma's bookshop has three different names: "Dinkley's Mystery Book Shoppe" on the window; "Dinkley's Mystery Books" on the sign sticking out; and then calls it "Mystery Inc. Bookshop" on the phone.
At the beginning, when the moat monster is unmasked, when he shouts, "I would have gotten away with it, if it wasn't for that big dog and you meddling kids." In this overhead shot, Scooby's paws are bare. In the next shot, the Moat Monster's mask is suddenly over one of his paws.
When Shaggy is packing the picnic for outside after Moonscar's ghost wrote the threats, he packed a sandwich that was way too big to fit into the basket. So Shaggy and Scooby ate the ends of it until it fell into the basket. But later, outside at the picnic, when Shaggy takes the sandwich out, it looks as though they never ate on the ends at all. (The bite marks are gone.)
When the Mystery Gang arrives at Moonscar Island, the sign near the dock is very tall. Later, when Shaggy tells Scooby to hurry up as he is picking peppers, the sign is much shorter than before.
The lobster-like monster crashes into a pile of cans that have white labels on them. Then when Shaggy takes its mask off, the white labels are gone.
When Lena shows Fred his room, she opens the shades to see the setting sun and tells him that he will have a great view of the harvest moon. The harvest moon is a full moon and would appear in the opposite direction of the setting sun. A moon in the same direction as the setting sun would be a new moon.
The Mystery Machine has been redesigned to be more like a minivan, yet in-universe, it's still supposed to be the same. However, in Scooby-Doo and the Cyber Chase (2001), Fred makes an oblique comment about it being good to be back in the old Mystery Machine while riding around in the Cyber Gang's van, so this can be seen as a joke. Also, as this series has a floating time-line, the video can also be seen as a reboot, not strictly bound to older continuities.
The glow on the cats' eyes aren't actually properly placed on their eyes but above them.
When Pierre brings the guys their sandwich, the basket of peppers looks more like soup. The basket is also irregularly in front of the item next to it, instead of sitting next to it.
When the alligator bites on the fisherman's pole, the sounds heard don't match it biting on it.