Audio problem: In the mansion, the boys open a secret passage and fall through the floor. They scream after shining a flashlight on a skeleton. Eugene then can be heard whining that he wants to go home, but his mouth is not moving.
Deliberate mistake: When the vortex is summoned to get rid of the monsters, other things get sucked into it. Cars, trees, light poles, other police officers. However other things or people who are more accessible do not get sucked in. For example, Phoebe hiding behind a bench, the bench itself, Phoebe's mother and a few cops hiding behind a cop car, etc.
Continuity mistake: When Horace is confronted by the Gillman and has picked up the shotgun, he looks inside and sees E.J. and another kid hiding behind the counter. Horace begs them to let him in. E.J. and the other kid shake their heads no and lower themselves behind the counter. A few seconds later, a distant shot shows the two shaking their heads and lowering themselves behind the counter again.
Continuity mistake: Phoebe is on the left side of the park bench as she watches Frankenstein fly into the portal. Just before it closes, you see Phoebe move to the very left side behind the bench. When it cuts back to the close-up of her crying, she's back where she originally was.
Plot hole: The army showing up at the end of the movie is wrong on numerous levels. 1) Eugene wrote and sent out the letter that day. I find it hard to believe the mailed letter got to the army in just a few hours time. 2) How did the army know to show up at time square? When Eugene wrote the letter, nowhere did it say where to meet. Plus the boys didn't decide to go to time square until the last minute. 3) since when is the army deployed to battle monsters based on a letter that was written by a child?
Suggested correction: The army's arrival being unrealistic is a very deliberate joke, like the armadillo-rats from earlier in the movie.
I submitted a category change to "Factual Error" to help cover this. It is indeed too deliberate to be a true plothole, but it is nonetheless amusing to point out all the ridiculous ways this humorous scene defies believability.
Other mistake: The werewolf gets blown to pieces by the dynamite, clothes and all. I can understand how the werewolf can reassemble his body as only silver can kill him. But how in the world do his clothes knit themselves back together?
Suggested correction: It was a nod to the comment Sean made earlier in the movie about Wolfman wearing pants in the 40's so you wouldn't see his "wolf dork"; it was meant to be a joke.
Plot hole: In order to get rid of the monsters, Phoebe needs to read a text from Van Helsing's diary in order to summon the vortex. As Dracula approaches her, she becomes scared and misses on some words (the Scary German Guy is helping her read since she is 5 years old and she doesn't repeat some of the words he says). However the vortex still shows up to get rid of the monsters.
Suggested correction: It is never specified that the incantation must be read verbatim to work.
It also never states that reading only part of the incantation would work either. However, the mistake is still valid because the way to get rid of something evil by reading some "spell" you'd have to read the entire thing. Therefore the virgin shouldn't have been able to summon the vortex.
Since "spells" are entirely made up and magic isn't real, you can't say that in this film every word must be read for it to work when the film itself shows otherwise. Every film gets to make it's own rules with magic, this film establishes that the incantation can be read "in spirit" to work. Other films might have different rules.
It's always been implied in movies and books that incantations must be read word for word in order to work. Otherwise, what's the point of having all the words there if you only need to read a word or 2?
Factual error: Horace was not holding the shotgun properly - the kickback would have not only made him miss Gillman, but it would have knocked Horace to the ground.
Other mistake: There is a lot happening at town square in the final scene; the kids are trying to get into the church, Rudy is killing vampires, and the German guy parked in front of the church. But in the overhead shot where we see the bat flying, there are no people or cars visible near the church at all.
Continuity mistake: When Wolfman throws one officer toward a car, the officer is shown leading with his left shoulder but in the next shot, which is a close up of impact, he hits with the right shoulder.
Factual error: When the silver bullets are being cast, the silverware thrown into the melting pot appears to melt instantly, the bullets come fully cooled and hardened out of their mold in seconds, and are already fully formed and polished, straight out of the mold.
Suggested correction: We only see Rudy put in a few pieces of the silverware, we don't know how much he already melted. The casts come out dull when he shakes the mold, what you are seeing on the table are the bullets he already made.
Character mistake: It doesn't occur to our heroes (admittedly kids) that you don't need to understand German at all in order to read it out loud. It's arguably easier to read than English! The only inscrutable letter would be "ẞ" but Scary German Guy's right there for help. (True, this is essentially what they end up doing in the end, but they still come about it through a "you don't need to be of age to be a virgin" realization rather than the even simpler "you don't need to know German.").
Plot hole: There are numerous problems with the final scenes in this movie. First, it's inconceivable that these kids are out at midnight at all; the boys are only 12 and two others are 5. Second, it took several minutes, possibly miles, to get from the house on Shadowbrook Road to town square, but the vampire mistresses make it there in mere seconds. Third, the sign in the store window where the two bullies are hiding said closed, so how did they get in? Fourth, Patrick grabs slack from the mummy's wrist but when the arrow pulls tight, he begins unraveling from the foot.
Suggested correction: Actually, Pete the dog took loose wrapping from the mummy's leg, and Patrick used that to tie to the arrow.