As the girls bed down for the night, Bubbles looks to her right and sees a clown doll sitting in the chair. In the overhead shots following, the chair is empty.
When Blossom was taking her test within her nightmare, she said that seven doesn't have a square root, because it's prime. Now, mathematically, the first part of her answer is nonsense. A square root can be calculated for any positive quantity; the only issue is whether or not that root will be a rational number.
In Bubbles' nightmare; she's in her bedroom where all of her toys come to life, become evil, and seize her. But later on, she's in a black void with the evil dolls preparing to turn her into a doll herself. But how did Bubbles get from her bedroom to a black void in the first place.
The advice to Bubbles to tell herself it wasn't real came from the fake Blossom, so how did the real Blossom know about it.
When Blossom finds out about HIM's scheme within her nightmare, Bubbles does not have the pink tulle at her hemline, and Buttercup's hands have no claws.