Oh. That's why. I stopped reading this a while ago, and decided to try reading again, and while I can certainly say it's not the worst, there are some things that just don't feel right about this. I think I held back with my criticism because I saw potential for this story. The premise was interesting and it didn't feel like there was poor grammar. In fact, you do use proper grammar and generally don't seem to have bad grammar. However, there's a problem: the dialogue. To be more specific, it's that the dialogue of the characters often feels inorganic. Sometimes it's poorly written. Sometimes, the text around it feels like there should be some more descriptive words. Here are a few examples.

"He tried to warn you, plus how did you not hear the shower running?" Twilight asks, looking up from her reading.

The pause one would put in between the two statements would generally be longer than a comma, and instead it would be more akin to the pause of a period. Along with that, the word "besides" would work better than plus, given what the words following are. Following the word "besides" (or plus, if you feel like keeping it) should be a comma.

"I still say you're disgusting, tainting cheese with egg, Heathen." Alexander states.

Now I'm just going to try restructuring this one:
"I still say you're disgusting with your tainting of cheese with egg, you bloody heathen." Alexander stays.

"Feel free to browse my fine wares. For you old friend, I might be willing to cut you a deal, 0.01% off." Jerry states with confidence.

This mostly works, but I would recommend placing a period after "deal" and replacing the period after "0.01% off" with an exclamation mark.

"Bad touch! Bad touch! Stranger danger!" Starlight hides behind Alexander.

This text seems to be meant as a joke, and it fails spectacularly because we don't see Jerry actually do anything that would warrant this reaction, especially from a former cult leader who ran a town of brainwashed ponies who acted very creepily and has also seen the world end by her hand. What I'm saying is that Jerry simply looked into her eyes while speaking with a different voice than usual, causing a massive over-reaction from someone who lived with a bunch of extremely creepy weirdos and has seen an apocalypse which she caused. It does not make sense, given what we know of the characters and their actions. Also, Jerry didn't even move to touch her, much less touch her. I know it's meant as a joke, but it does not work as real dialogue. Sure, she could be creeped out, but shouting "bad touch" and hiding behind Alex doesn't make sense given everything we know. If you want to show her being freaked out enough to move away, I suggest something like this:
"Ah!" Starlight shouted, jumping backwards.

Of course, if that change occurred, a change here would also need to occur.

"Well, that was interesting... Why do you always have this effect on people?" Alexander asks sighing deeply as he looks over the wares.

Here, I recommend replacing "Well, that was interesting..." to something along the lines of a sigh or the word "ah..." to make him seem disappointed in some way.

I'm always happy for criticism so long as it's constructive, unlike some comments I've got before on other fics just outright shooting down the story premise because of blah blah rather then taking into account the world it's being told in. Looking over most of what you've said I can agree with the majority of the criticism. As for the bit about Starlight's reaction. That wasn't serious dialogue to be honest. Jerry's line along with her response was a reference to JonTrons reaction to the brown ferret or whatever when he watched Food Fight. I will most certainly go over what you've said with my co-author and see what he thinks about the criticism. In general though I thank you a lot for taking the time to post such a constructive comment. Sincerely, thank you.

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Hey there! We used 3 out of 5 of the grammar corrections that you made. Now I will mention what we didn't include or fix.

"Bad touch! Bad touch! Stranger danger!" Starlight hides behind Alexander.

Now as we write this story we brainstorm ideas and incorporate memes into the story as a whole. This is a direct reference to JonTron who I will leave the video of the part where he gets his reaction.

Now for the last one:

"Well, that was interesting... Why do you always have this effect on people?" Alexander asks sighing deeply as he looks over the wares.

Alexander and Edward are their own characters, which is a personification of my partner and myself. If anything Alexander wasn't disappointed, he was amused. Also, there is already a sigh at the end where he asked.

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Sighs are indicators of two things: disappointment and contentment. Amusement is expressed through smiles and giggles.

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"Well, that was interesting... Why do you always have this effect on people?" Alexander asks as he chuckles lightly while looking over the wares.

I changed the before debated line to have this alteration at the end. I chuckle in amusement a lot at some things.

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You do know she never caused that apocalypse, right? That reality existed before Starlight traveled through time.

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When I speak of her apocalypses, I speak of the episode in which she messed with time. Because she went back in time and messed with the timeline, various "bad ends" occurred, including one in which everything to be seen was a barren, blackened, ash-covered, wind-swept waste with not a sign of life in sight. Is that or is that no an apocalypse that she did not directly cause by changing the timeline?

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8548514
I feel and want to say you're both right, but I lack the proper words to actually explain why I believe this. I also would say that perhaps the timelines were created as a direct result of Starlights tampering with time but like I said I lack the proper words to adequately explain what's inside my head. So, I'll more or less stick with that I feel you're both right.