A screenshot of an email death threat to Hideaki Anno from angry fans and a picture of the vandalized Gainax office building are among the random images played toward the end of the film.
According to Misato, the computer screen she is viewing near the beginning of the film is a file which reveals the truth of Second Impact. In reality (from what is legible) it is nothing but a short bio on Gainax and its films.
The film was based on the scripts Gainax originally intended to use for episode 25 of the TV series, but were unable to due to budget and production problems, and TV Tokyo's refusal to allow the episode to be produced for television broadcast. The second half of the film builds upon the script to create an ending concurrent to the one shown in the TV series.
The red dummy plugs we see injected into the Mass Production Eva series before they launch are labeled "Kaworu".