>What are you referring to here? It was her magic she used to remove their cutie marks, no? The second part refers to Double Diamond being able to get the cutie marks from the vault somehow, though, and that is a very, very good point to make. Also, what are these external forces you are referring to?
1) She needed magic to remove cutie marks, and when they're not magically restrained, they fly off. There is the consistency that although it is a "vault", it is glass, plain glass. The jars also restrained the cutie marks.
2) how did the non-magic-using pony collect the cutie marks into jars, and open the glass, presuming he did not use magic? The others had to break into the vault, literally.
3) External factors. So far we haven't had a villain which dispatches episodic minions. Reasonably speaking that's a possible upcoming villain. She could have been holding the cutie marks as some source of power for another character, or even could have been fooled herself, by the greater villain teaching her the cutie-mark stealing spell, so they would eventually have them for themself.
If she was taking cm for herself, she'd be more inclined to have a kinda fetish for them, which she did. If she was a minion, she would've been likely to keep the most power more secure, or even show regret or wariness from holding the "most powerful" marks with her.