After Domain talks about a God of Death, ancient fourth-dimensional demons hidden from Xibalba and a super-civilization psychically enslaved, the second book forgets about such god, reveals there is no other demon that the Nephilim themselves, and Retcons away all the flashbacks about their enslavement (they were never mentally controlled by a mysterious figure come from the sea the way it is portrayed, for instance, but simply chieftained by Lilith and Devlin, who were already their chairmen), as well as changing Xibalba itself (which is now not a lush planet, but a Death World with a floating high-tech continent). To put it simply, the setting changes so much from the first book to the second that it might be perfectly a completely different story, and nothing about those changes or purported revelations is ever lampshaded in the first. The presence of plot points like the space signal that activates the Tezcatlipoca ship, which couldn't exist with the revelations given in Resurrection, might imply we must treat the whole first book as Broad Strokes.
Jacob suddenly becoming a spirit of light who solves all of the final battle in Xibalba after being killed by Devlin. There's no foreshadowing for this and it comes a bit out of nowhere.
Several, if not most of the plot points given in the book, either come completely from nowhere or directly contradict established events from the previous books. The most blatant are the LHC being the source of the wormholes (which were supposedly to be natural events), Manny being the reincarnation of an ancient Hunahpu (something that even vaguely contradicts Phobos itself when they claim he and Jacob share a soul), Rafelo being controlled by another ancient Hunahpu (despite it had been left very clear that he was just a figment of Lilith's imagination), Lilith being claimed to have been literally unable to love in the past (even although she explicitly loved Jacob), Julius' work now having something to do with the Hunahpu-aliens (who weren't even present in the previous events), the entire character of Chicauah (and her knowledge and powers) and the Kabbalistic universe and all its mystic, divine influences.
The books hammer down that every event in the past causes deep changes in the future and vice versa due to the Stable Time Loop, which is the reason why they cannot simply change events without risking themselves to change the past and then the present. In Phobos, after Manny changed the future, there are no Balam and Tezcatlipoca ships sent to the past and found in the present, meaning the planet could not be saved from the LHC... only that, with the instrumental role in the history of mankind played by both ships and its crews, somehow this new timeline is almost identical to the previous when it should be a completely different human civilization, without the influence of figures like Kukulcan and Osiris, and without all the wars and holocausts caused by the Tezcatlipoca's Hate Plague. In fact, considering the LHC is informed to have been created by human ego and the latter was stimulated by the Tezcatlipoca, changing the past that way should have impeded or at least delayed the creation of a similar thing.
Also in Phobos, it is explained that wormholes are somehow bonded to the Earth, meaning that after the planet is destroyed by the strangelet, the next wormholes have to lead necessarily to the past as there's no future remnant. Considering that very book explains the wormholes are random phenomena caused by the LHC, which would give no reason about why they cannot simply appear in the space next to the destroyed Earth, this rule comes across as an obvious Hand Wave meant to explain why the wormhole to Xibalba from Resurrection now leads to Julius' era.