Broken Base: The feuding among fans about which Expanded Universe works or sub-continuities are good and which ones are horrific parodies of the franchise that don't deserve to carry the name. The factions can be divided according to a scheme invented by the writer Gareth Roberts in the nineties, which has two orthogonal axes. On the one axis you have "Rads", who like works which do things that would never happen on the TV show, whether that involves spectacle that would have never been possible on a BBC budget, modernist or post-modernist experiments with form or style, or explicit exploration of sexual relationships; versus "Trads", who want works that could plausibly have been made as normal TV stories in the era when they're set (this is analogous to the non-fandom-specific typology of fanfic and its writers as "more from" versus "more of"). On the other hand, you have "Guns", who want stories set on Crapsack Worlds in which everybody is a complete bastard including the Doctor and everyone except the regulars dies as gruesomely and graphically as possible, with it being very unclear at the end if anything good might have been achieved; versus "Frocks", who want stories with happy endings and lots of jokes. There is a slight bias towards the Rads-Guns and Trads-Frocks regions of the graph, but significant numbers of fans can be found in all four quadrants.
Darkness-Induced Audience Apathy: Some of the writers seem to make a point of undoing as many happy endings from the TV series as possible, as well as killing off TV characters. This is particularly an issue in the prose Seventh and Eighth Doctor novels, and latter-day Big Finish.
Ship Tease: Various expanded media have been freer at giving the Doctor romantic relationships or amplifying ship-teasing already in place on screen. For example, in the BBC Books novels, the Eighth Doctor gets married at one point; the Big Finish audios allowed ship-teasing between various incarnations of the Doctor and companions including a never-thought-of shiptease between the Fourth Doctor and Leela; and the 2015-2016 run of Titan Comics' Twelfth Doctor comic book was notable for cranking the UST between Clara and the Doctor Up to 11.