yeah in fact Mega-Diancie put it best in the comments of the last chapter of What Have You Done? and cloudedguardian put it best in the comments of the sequel Even As...
-Back when Discord tested the Mane 6, Rainbow chose Cloudsdale over her friends. Loyalty didn't have an issue with this. She had to pick one or the other, and she had loyalties to both that were precious. She chose Cloudsdale. That was fine.
But then Rainbow Dash rejected Loyalty. He didn't understand the why, but rather that she felt like she was no longer worthy. It took Twilight reminding Rainbow of her worth before he was accepted back as her Element.
Then the wedding comes. Rainbow Dash chooses Cadence over Twilight. A Princess she has no loyalty with over her best friend. It may very well be that Loyalty still doesn't understand the why, but he knows one thing- Choosing someone else over friends equals lack of worth. Rainbow herself made that quite clear. But this time, there aren't any other precious loyalties, no wiggle room for forgiveness. And so Loyalty rejects her
-Rarity was looking for praise for her dresses, her chance to be a bridesmaid, and a chance to suck up to Canterlot higher-ups. Something that is normally greedy for most of us as we would normally feel it if we were in her shoes, but she abandoned Twilight and chose the wedding over her, thus her greed over-shined her generosity. and so Generosity rejects her
-Applejack promised to take Twilight more seriously whenever she was worried and to listen. But all she simply thought Twilight was being silly and refused to listen to her at ALL, which helped drive Twilight to making that confrontation in the hall as no pony would listen. And like that, a promise became a dirty lie. and so Honesty rejects her
-Pinkie Pie was so concerned with her views of making sure the wedding was a happy time and seeing the good in the world while ignoring the bad, she failed to realize that Twilight was in dire need of comfort and hope, even thinking of her as a 'party-pooper'. Laughter means cheering up everyone who needs it, not just deluding yourself into focusing on the happy stuff and ignoring the bad. So by the time Pinkamena made her realize, it was already too late and so Laughter rejects her
-As for Fluttershy...ignoring other's concerns, failing to realize someone is being cruel towards somepony and towards her birds due to the wedding or flat out ignoring it, and flat out abandoning a broken pony, choosing the wedding over her...That's even more cruel then she was than she was in 'assertive mode' and so Kindness rejects her
As for Magic's words: Its understandable. Twilight's friends threw her away, sending her into despair. Now Magic is in despair because Twilight has turned her back on it due to her depression.
also Trixie was right in Turnabout Storm about Friendship and I'm sadly agree with her
“There’s no MAGIC in it—it’s just a word, nothing more, and it’s completely unnecessary."