Development Hell: The site has undergone many projects that would have improved on stability and user interface, but none have ever been completed; some projects, even to this day, are still going through years of development. Most long time users roll their eyes whenever the admins announce a new feature or layout they have planned because the users know that said projects or improvements will never get finished.
Executive Meddling: 2010 saw an unconditional ban instituted against so-called "cub porn" (underage anthro characters depicted in sexual activity); the admins said that the ban was not so much because of the content itself, but because FurAffinity's advertising sponsors were starting to cut funding off.note Cub porn would have most likely been viewed as child pornography, which is an ''extremely'' serious issue for most of the world and advertisers would not want to be associated with such things.
Not unique to furry art, FurAffinity, or art in general. There's always someone who will commission something then nitpick a detail and repeat until the artist gives up on them, and then post every individual sketch as 'art I commissioned from X', as well as people who copy the art and claims it as their own ('tracers'), or takes it wholesale and posts it without attribution ('assholes').
Commissioners who had been taken advantage of may fight back by either raising the prices of their art or making it much harder for other people to get a commission from them. The action screws over everyone else that would have been a normal paying customer.
Sometimes, artists that are drawing things for the community at large (whether by free requests, interactive projects, etc.) get taken advantage of and said artists will then stop taking ideas from people or even scrap their projects entirely. It's not unheard of to see a series of art that won't progress any further ever again due to the artist not wanting to deal with the greedy community groups.
Even trying to get in touch with an artist on a personal level can get sour at times. It's not unheard of for people adding artists to their friend list on various chat clients and then trying to flatter the artist while also mooching off of them for free art. If it's not for the art, then some furries try to add other people to their friend list for sexual role playing only; despite what many people will tell you, not every furry is into sexual fantasies.