Fridge Brilliance: In Chapters 1 and 2, Blaineley was "tricked" out of the game by Celestia and Luna because they were afraid she would expose the secret as long as she was around. In Chapter 13, Celestia and Luna were indeed correct, though not in the way they thought.
Moral Event Horizon: Scott crossed it in Chapter 18 when he almost raped Dawn. You can also say Tuerto crossed that line once he accepted the Cutie Mark Pool's essence.
Nausea Fuel: In Chapter 11, the Total Drama gang was seen eating grass. Now, think about this for a minute. In the world of 'My Little Pony', there are no bathrooms, no toilets... so, where do you think the cast go to the bathroom in? The Total Drama cast thought about that, and was seen spitting out that grass.
On the other hand, both outhouses and indoor bathrooms have appeared in canon, so the nausea factor is mitigated somewhat.
One of Us: Orange Ratchet must be familiar with TV Tropes as several characters use tropes verbatim or at least are aware of them.
Special Effects Failure: Lampshaded by Heather, Gwen, Leshawna, Trent and Eva when they meet up with Troll for the first time... but that doesn't mean Troll and the Puppeteer can put up a good fight.
The Woobie: Despite Chris' jerk tendencies, in later chapters, after realizing what he had was gone (losing Blaineley and putting the contestants in danger), he is at least attempting to be nicer to the contestants. Doesn't mean he'll pull the occasional prank every now and again.
Also, instead of Pinkie and Izzy giving the small poem that gave the prediction of Tuerto's back, had Mike had kept his personas at the end of Total Drama All Stars, a new one in the form of a psychic predictor would have give the prediction instead.
Instead of Leshawna, Dakota was originally going to be part of the group that was on the quest to find Tuerto's eye. However, because Leshawna was written more with a couple other characters (Gwen and Heather), that had been changed.