Base Breaker: Two huge bombshells drop in this TV movie that have divided fandom for 20 years:
The Doctor says he's half-human on his mother's side. This continues to be controversial with some expanded media suggesting the Doctor uttered this while under post-regeneration psychosis, and the 2015 season finale also played with it. One reference work on the history of the series, Electric Gypsy has the author state outright that he does not consider the movie canon because of it.
The Doctor kisses Grace. This triggered a ton of backlash from fans who felt romance had no place in Doctor Who. To this day some fans blame the film for setting the precedent that led to the Doctor romancing the occasional companion and guest star in the revival, and the show itself has actually lampshaded the controversy on several occasions.
Big Lipped Alligator Moment: A cop on a motorcycle drives into the TARDIS and comes out moments later to go god-knows-where while the Doctor and Grace look on.
The Doctor, upon regenerating inside a morgue—specifically, in a cold chamber, while an orderly is outside watching Frankenstein. Somehow, the new, very confused Eighth Doctor kicks down the morgue door, attracting the attention of the orderly, who walks in, sees Paul McGann walk out wrapped in a sheet squinting at the heavenly light surrounding him. The orderly takes the only sensible recourse, and drops in a dead faint.