Keep Circulating the Tapes: Many of their older releases have started going out of print as of recently. They have responded to this, however, by releasing complete collections for Puella Magi Madoka Magica and Durarara!!, and re-printing the standard edition DVD releases for Fate/Zero. However, releases such as the Blu-ray of Baccano! have not seen a reprint.
Limited Special Collector's Ultimate Edition: They're rather fond of using bonus content as a way to jack up the price of their DVDs to obscene levels—usually around $80-$90 for a twelve-episode show and $140-$150 for a 24 episode show.
However, nothing comes close to their imported Blu-ray edition of Tengen Toppa Gurren Lagann, which was sold for $550 for a 27 episode series and two movies!
They're now[when?] creating their own domestic release of the Blu-ray set, individual Special Edition volumes, $50 ($60 if not bought through their preferred online retailer), 5 episodes a disc, no Vanilla Edition.
They topped themselves again with Kill la Kill, which features a single four-episode volume with an MSRP of $76 (though through their retailer of choice Right Stuf, they even out to $60). The Vanilla Edition Blu-ray is still $40 for the same amount of episodes, and the DVD is still a crazy $30.
No Export for You: The fate of some of the more obscure shows in their catalog. There are many shows they've had licensed for years but have never seen the light of day on a home video release and are only available via streaming.
Canadians has it worse since they never exported any of their series outside of streaming services like Netflix. Meaning that if you want a physical copy of Sword Art Online, you have to pay extra for shipping.
Production Posse: All of their English dubs are produced by Bang Zoom! Entertainment.
Screwed by the Network: Beginning in 2016, Aniplex USA decided not to have Funimation renew their shows.