Gameplay and Story Segregation?
It is what it sounds like it is. It's when something happens in the game because it would make the game better, not intending to affect the story. From my experience, 85% of grievances with Halo's storyline usually comes down to this.
In the novels, the Master Chief can run 60 Kph. Why does he barely trot in the games?
All of these questions pretty much have the same answer: The developers did not want to sacrifice a fun experience for the sake of the story. Most of these can be disregarded... most of them.
In the main Halo trilogy, the Grunts and Jackals could not be made into Combat forms because they were too weak, yet Halo Wars has infected Grunts and infected Jackals
These forms were added because of the need to balance Flood threat between UNSC marines and flamethrower troops and Covenant Grunts and Jackals. However, since nothing has been said about them from developers, is this truly a retcon or something to overlook? Perhaps this Proto-Gravemind tried to assimilate Grunts and Jackals into Combat forms, failed, and the Flood as a whole never bothered with it again. It could work.