(at around 13 mins) When Verne first left the group to cross the hedge, he came out in a backyard. However, when he returned to the forest, he entered the hedge from a road, but ended up in the same place he left from, in front of the group.
(at around 1h) When Heather gets kicked down the stairs by Gladys, Gladys has a coffee cup in one of her hands. However, when Gladys walks halfway down the stairs, she's not holding a coffee cup.
(at around 15 mins) When Verne gets hit by the bike and hockey stick and goes through the hedge, there's no tire track on his shell while flipping through it until he shows RJ the bike track.
RJ caught the grappling hook on a root and left the hook there after pulling himself up. Later, the root disappeared, and although RJ never returned for the hook, but left for the town right away, he still had the hook and used it several times.
(at around 1h 8 mins) Before being pulled off the Verminator's van, Vincent severely scratched the roof with his claws. Later (when the van crashes into the house), the scratches have disappeared.
Many of the animals depicted as hibernating don't actually hibernate (including the squirrel).
Many script details emphasize the point that Tiger is supposed to be a Persian cat, describing his recessed nose, his proud lineage, and talking with a Persian accent. Yet, the animated cat is clearly Siamese in design.
Turtles cannot be separated from their shells, which are fused into the spine.
It would've taken more than a season to remove woodland to make way for a suburban area.
RJ tells Hammie he should pretend to be rabid and scare the Girl Scouts to grab the Girl Scout cookies. The Girl Scouts panic and grab their guidebook which tells them how to deal with rabid squirrels. Here's the thing though...squirrels don't carry rabies.
(at around 1h 1 min) Stella and Tiger get into the house, even though they didn't have Tiger's collar to unlock the cat door. This is because the collar was left by the cat door to keep it unlocked while the animals sent the food out through it.
(at around 1h 1 min) When Stella re-enters the house upon hearing the emergency, her white stripes mysteriously reappear, exposing her true species to Gladys, and showing to Tiger the Cat that she's really a skunk. However, the reappearance is no mystery. When Stella comes through the cat door seconds earlier, there's a puff of "smoke" -- which is from the charcoal dust that was used earlier to hide her stripes.
(at around 30 mins) When Verne's shell falls off, his tail is missing.
During the climax while hiding from Vincent on one side of the hedge and Dwayne and Gladys on the other, Dwayne is able to shock Vincent on the other side and gets attacked back, believing it to be the animals in the hedge. Why would he think that, since such as slap can only be done by a bear, something much larger.
The gang wouldn't have been able to bring the items through the hedge easily, judging how big they are and how small the branches within the hedge are (which the animals judging their size are able to get through alright).
It's unknown how Stella got inside the birthday cake.
(at around 2 mins) When RJ first sees Vincent's cave, it's atop a sheer, vertical cliff (so sheer he can't climb it and has to use the fishing pole to gain entrance). However, moments later, when the wagon of food gets bumped out of the cave, it bounces down a more sloped hill with lots of ledges and rocks.
(at around 18 mins) When RJ opens the bag of chips, it creates a large puffy cheese cloud that can be seen from space, like around Seattle. (at around 1h 12 mins) However, when the Depelter Turbo activates, a beam shoots out into space, but it comes from somewhere near Chicago.
At the start of the movie, there appears to be no signs of snow starting to melt, which does appear the next morning when we see Verne awaken from hibernation.
When RJ left Vincent to save his friends from the Verminator's Van, the collision with the cart of Food for Vincent sends Dwayne unconscious, and freeing the animals from their cages, yet, when that happens at the start of the film, nothing happens to the vehicle that crashed into the food.
It would have taken much longer to build the 54 acres of homes than the animals hibernated, so there's no way they couldn't have known what was going on around them.
No explanation was given is to how Vincent was able to find RJ after waking up once the Full Moon had arrived.
(at around 1h 18 mins) During the end credits, Hammy talks about the Genesis Device from Star Trek II: The Wrath of Khan (1982), and incorrectly states that the Device was carried on the USS Enterprise.
(at around 1h 9 mins) After crashing into Gladys' house with Dwayne's van, Dwayne begins to regain conscious, and breaks his back as he reaches out for the animals just they escape back to the woodland in time. Yet when he and Gladys arrive with tools to fight off the animals, Dwayne appears to be fine.
In an interview for the film Allison Janney says that Gladys is the 1st animated character she's ever voiced but she obviously forgot that she voiced Peach the starfish for Pixar's Finding Nemo. (not kidding)
RJ never thinks to unleash the viciousness of his species upon Vincent.