Base Breaker: While the novel itself is near-universally despised, fan opinion is divided over the revision (which still hasn't materialized). Some fans are optimistic about the revision and hold BioWare to its word, others point out that the novel's problems run far, far deeper than the continuity errors and that just fixing the lore errors isn't good enough to redeem Deception (specifically saying you'd need a total start from a blank canvas with a new writer), and then there are those who feel that the promise of the revised edition was just damage control and it will never actually happen.
Canon Defilement: There is a list of its many, manycontinuity errors as linked below. Let's just say it'd be easier to make a list of what it got right. Good thing later editions will fix these problems... hopefully.
Kai Leng eating Anderson's cereal. The inevitable "cereal killer" jokes don't help. Neither did the text stating that he did it because he was "an adrenaline junkie and enjoyed being where he was". Leng eating Anderson's cereal was actually highlighted on the forums as a moment to be kept in the revised edition because it's so utterly hilarious. And frankly, Leng is so petty even in the actual games (see: him sending Shepard insulting e-mails in 3) that it's actually quite in character for him.
Kai Leng "was about to pee in a vase that he had selected for that purpose". Yes, that happens. In those exact words.
Gillian's death. It should be tragic, but there's something inherently funny about the fact that Kai Leng is killing her with a toothbrush.
The numerous errors regarding the lore of the Mass Effect universe led to this Google doc, this forum thread on the BioWare Social Network (which reached 456 pages), a video of a Mass Effect fan burning his copy that made the rounds on a few gaming websites, and this open letter on the Mass Effect Wiki. Days after the book's release, BioWare announced that a revision would be made.
Suffice it to say that a number of autistic and LGTBQ readers weren't pleased with the depicitons of autism and homosexuality. Specifically, that a character who was autistic in previous books "Outgrew it" (which is impossible), and a previously established homosexual male character was turned straight, and then killed.
This book gave Kai Leng the infamous "cereal killer" nickname.
The writer isn't very likely to escape being "that guy who wrote Mass Effect: Deception" any time soon.
They Just Didn't Care: Even after their apology, BioWare still get accused of this for approving the novel in the state it was in. Especially since the writer claims two BioWare officials did look it over.
What an Idiot: Late in the novel, Hendel threatens biotic harm on Aria in the middle of her private room in Afterlife. He's damned lucky all she did was tase him.