When Winnie is riding on her broom and pulls alongside Max in the driver's side as he is racing away from the Sanderson home after saving Dani, she asks for his driver's permit. As she died 300 years previously she would have no idea of drivers permits. Or even of cars.
The Sanderson sisters often refer to cooking with margarine. They died (for the first time) in 1693. Margarine wasn't invented until the 1800s and wouldn't be available as a butter substitute until 1869.
At Allison's house, Dani is surprised to find out that there is a museum about the Sanderson Sisters. However, when Allison leaves to change, Dani says that her friends at school told her all about that place, meaning she had to know it was a museum at one point.
During the adult's Halloween party scene, Dani tries to tell her mother about the Sandersons, and Jenny, thinking she's just on a sugar high, asks "How much candy have you had, honey?" To which Dani replies "I haven't OD'd! I haven't even had a piece!" This is a lie. She had a chocolate witch lollipop at Allison's Halloween party earlier, though she could've forgotten with all the excitement.
When Dani first finds her mom at the town hall party, the mom is "vogue-ing" with her right hand on her head and her left hand stretched out. As the camera cuts back and forth between the mom and Dani, the mom's wedding rings disappear from her outstretched left hand.
After Max lights the candle, and things start to happen within the house, Dani's hat is blown off by a gust of wind. When she puts the hat back on, her hair has been blown around. When the camera cuts to her again, her hair is back in the style it had prior to her losing her hat.
When Max and Dani go into Allison's house to trick-or-treat, as the conversation carries on, Allison gives Dani a large witch-shaped sucker. A few lines later, the witch sucker she holds changes to a much smaller, differently shaped sucker.
When Billy first reanimates, his grave is shallow - only deep enough for him to lie down in - and in disarray. When they return to the graveyard, his grave is suddenly a perfectly dug hole deep enough for Dani to stand all the way up in.
When Winnie is giving instructions to Billy, the broom handle is crooked when we see her from the front with a flat top of the handle. When the camera view is over her shoulder, the handle is straight and modern-looking.
When the witches arrive at the school, the clock in front of the building has just gone 3:05. Later when the kids are dancing in front of the building, the clock reads dead on midnight. Then later on, right before the witches run into Jay and Ice, Ice mentions that it's 3AM.
Before they go trick or treating, Dani tells Max that there is a full moon out. The movie is set in 1993, but the last time there was a full moon on Halloween was in 1974. The next will not occur until 2020.
The real Salem witch trials began during the first few months of 1692, and were finished by the October of that same year, though in the movie they state that the Sanderson sisters were hanged on October 31st, 1693.
Many people think that it's a plot hole that Winifred is able to stand in the cemetery at the end of the film, as Binx had said that witches aren't able to set foot on hallowed ground. This isn't a plot hole. Standing on hallowed ground is why Winifred turns to stone before turning to dust. Binx said that they weren't able to stand on hallowed ground, but he never specified what would happen to the witches if they did or if it would be instantaneous. So, in the context of the film, it makes sense that Winifred was able to stand on hallowed ground, even if only for a few seconds.
When Sarah Sanderson sings her song to summon all the children, it is way past the time for them to be in bed. Yet, when we see them all following her, they are still in their Halloween costumes. Many parents are likely to let their kids sleep in Halloween costumes since they only get to wear them for one night. Addtionally, many parents were at the Town Hall party, so the kids would have had little, if any, supervision.
In the beginning of the movie Emily is lured to the Sanderson house by Sarah's singing. Thackery and another member of the village hear the song and follow Emily to the sister' house. How were Thackery and the other young man not hypnotized by Sarah's song? Even if they were "too old", Thackery's age doesn't stop Mary from "smelling" him and identifying him as a child when he sneaks into the house.
When Max first gives Allison his number, it is on the top left corner of a piece of notebook paper, where the holes are clearly visible, once they are outside and she returns the folded up piece of paper, you can tell that his number is now on the opposite side because of how it's folded.
After the witches are burned at the school and the kids return home they enter the dinning room. They call for their parents and if you look in the glass on the left you can see crew and the pole for the mike moving.
The witches take Emily in the morning, However they are hanged (supposedly soon afterwards) at night. If it only took Thackery a short time to follow Sarah and Emily to the house then it shouldn't have taken the town folk the better part of the day to arrive.