The original voices for the cartoon were added via text-to-speech software as a placeholder. This meant the actual voice over work by the actors had to be lip-synced in post-production and caused nearly a weeks worth of work to match the voices to the mouth movements.
During Spider-Man's hallucination, Deadpool was going to explain in greater detail why "None of this is real" and physically show him by walking outside of the cartoon, that they were just in a badly animated cartoon on Youtube. This scene was not created due to time restraints.
The theme song of The Badly Animated Spider-Man is an instrumental hard rock version of the original Spider-Man cartoon theme. However the first few notes of the song are an homage to the 90s Spider-Man cartoon.