Continuity mistake: When the class is in Arnold's esophagus, Tim says something, then it cuts back to Ms. Frizzle. Arnold is sitting in the back seat of the bus.
Gets Ready, Set, Dough - S1-E9
Continuity mistake: In the scene where the kids are getting the ingredients for a cake, the list of ingredients in the cookbook changes between shots. In one shot, the flour is at the top of the list, and the eggs are right below it. In the next shot, the eggs are at the top of the list, and the flour is below it.
Continuity mistake: After Phoebe shrinks the class, Wanda's clothes change from red to green.
Answer: In general, quite accurate as that was the point of the show. To teach kids about science. As the show is now over 20 years old, some facts have changed as we're always discovering new things. For the time, it was as accurate as it could and much of it is still accurate now.
One thing I think the show gets wrong is the idea that electrons stop moving when you break a circuit. Electrons never stop moving.