Actually screw it. This is a discussion thread, no more spoiler tags.
Yes there are a couple
1. There are allegedly only 2 CAS-class assault carriers in the entire High Charity Defense fleet, both at the start of the battle, Sangheili held...ridiculous considering Truth himself had 2-3 at the Ark. Additionally H2A shows several in orbit during the battle. Now if you consider the Battle of High Charity and the Battle of Installation 05 separate that could be rectified however (the wiki does this).
2. Half-Jaw glasses the city of High Charity, like in the dome to prevent flood infestation even though the Flood not only survives but has completely consumed the city.
3. The Shadow of Intent is crewed by some 200 soldiers due to 'limited recruitment'.
- This is slightly more bearable because Thel wanted to make sure the vessel was kept out of his enemy's hands and we know in Escalation how easy it is for traitors to emerge *cough Sali *cough. And there were traitors even in his camp and keep lol. So it makes sense for him to send Rtas on a long range mission with a small crew to keep it out of harms way (easier to screen 200 than 200,000) still the number was low and could have been explained a bit better than 'war killed the rest of the crew'.
4. SoI is the only assault carrier in the Swords of Sanghelios fleet. This is simply false. Even in 2559 based on the Return we see at least one other (if not more) assault carriers still in the SoS's fleet. There were a few other minor ones as well like an assault carrier only having seven plasma cannons and stuff.
5. And this is perhaps the big one. Shadow of Intent is stated to have started in Sangheili hands and Rtas is heavily implied to be aboard in the opening hours of the Great Schism when the Brutes betray the Sangheili. We know this to be false as Rtas was present on Installation 05 leading quarantine operations on the ground, then he is seen moments before the Arbiter's betrayal at the library. Then finally he's seen at 05 telling the Arbiter he'd take a cruiser back once he helped him reach the Scarab. + SoI is said to have started in Jiralhanae hands and taken back by Rtas.
"Very little is known of the Shadow of Intent’s operational history before the Great Schism. However, at the start of the Covenant civil war it was seized by Jiralhanae forces and turned against the Sangheili fleet staged outside High Charity. As the Arbiter fought to stop the firing of Delta Halo, special operations commander Rtas ‘Vadum led a strikeforce aboard the ship to retake control."- Waypoint
There's also the uber Grunt who I personally love, but some might find to be an offense to the canon.
"Stolt had survived encounters with human soldiers that saw many of his comrades fall. When he wasn’t battling the enemy, he outfought any Sangheili who sparred against him, enduring their melee strikes until they tired, and then pummeling them into submission with his chitinous fists and feet. After a chance encounter with one of the humans’ fearsome Spartans, in which the Unggoy wounded the enhanced human so grievously that it was forced to withdraw, even the Blademaster approved Stolt’s promotion to ranger leader."