When Remy crawls through the barricade she falls down the other side and is wearing a G-string. A short time later when she strips off her clothes she is wearing totally different underwear.
In the opening scene, a (presumed) bug limb slashes through the roof of a taxicab, but when we later see a shot of the crashed cab from above, the roof is intact.
In order to give his shirt to Remi in the principal's office, Nicky first takes off his jacket and lays it on the floor. He then backs up halfway to the office door, where his jacket reappears.
At approximate 44 min Remy states incorrectly that the Judas Breed began as a genetically modified cockroach. In fact, according to Dr. Tyler in the first movie, they were genetically engineered from a hybrid between a mantis and a termite.
When officer Klaski arrives at the school where Remi and the two boys are trapped, he finds entrance bolted and cannot enter. However, a few minutes later, when Remi is about to be killed by the creature inside, he appears out of nowhere with his gun blazing and saves her. There is no explanation as to how he managed to gain access to the school's interior.
At about 1:01:30 into the movie: When Detective Klaski confronts the CDC agent outside the infested school the CDC agent addresses him as Detective even though Klaski is in plain clothes and hasn't yet identified himself. Nor was the CDC made aware that he or any police officer was on site when Remy called to report the infestation earlier.
Correction: The CDC agent that addresses Det. Klaski, is one of the agents that was crawling around Remi's apartment building, with the lights following the trails. He knew who Det. Klaski was because they had already met.