This is just me listing out the differences between the games' canon and the novel canon.
1.In the novels, William Afton is the Purple Guy and is the one who becomes Springtrap. However, in the games, there are two Purple Guys and William Afton was the Purple Guy in the MCI Freddy Fazbear's while Michael Afton was the Purple Guy in Five Nights at Freddy's 2-4. Michael is also the one who becomes Springtrap in the games as well.
2.In the novels, the child who becomes the Puppet is Henry's son named Sammy. However, in the games, the Puppet is actual the kid we play as in Fnaf 4.
3.In the novels, the Bite of '87 never happened.
4.In the novels, Shadow Bonnie/RWQ is Henry posessing an animatronic based off of Theodore. In the games, however, Shadow Bonnie was actually an employee that was killed in Fnaf 4 by Michael Afton.
5.In the novels, Golden Freddy is the child whose name is Michael Brooks. In the games, Golden Freddy had a different backstory entirely.
6.In the novels, William Afton never had a family. In the games, William Afton had four children.