"Well haven't Rarity and Rainbow Dash been spending a lot of time together lately?" Twilight asked as she noticed that Rarity and Dash were spending more time together than normal a little while ago, not thinking anything of it at first, but now since they seemed to be going off together more regularly, it caused her to become a little sceptical.

It’s ok for a paragraph to contain more than one sentence. It really is, I promise. If 100% of the sentences in this story aren’t too long, than at least 98% are. You say the same thing over, and over, and over again, almost to the point of parody. Please read what you have written and try to trim away what isn’t necessary.

To clarify, I’m quoting one of your many, many run-on sentences. This is not the worst offender in terms of redundancy, but it needs work there too.

"Now that ya mention it, I have seen Rainbow Dash going over to Rarity's a lot lately, especially in the evening," Applejack stated as she thought back and now did realize that she had seen Dash making her way to Rarity's a lot, unsure of what the reason was, and always thinking it was a little strange for the cyan pegasus to be going over there so much.

Look at this bloated mess of a paragraph. It should end with “…Applejack stated.” Nothing that follows imparts any new information. Are you paid by the word or something?