It's very simple.
The events of the movie happened. The events in Citizen Ghost after the movie happened.
Like Doctor Venkman said it was meant to be an inside joke, but a lot of people, myself included, took that as an definative statement of the placement of the TV series and movie in conjunction with each other. Ya, I know I think to much into these things.
Anyway because of Take-Two one could assume that in the cartoons universe, the events of the movie happened, just not 100% as they appeared in the movie. The events of Citizen Ghost happened later and eventually Take-Two where the movie was made about the events that we know now as the “first movie”
…Like Doctor Venkman said…its complicated.