Given I work in the field in question, I think I can provide some perspective on this issue?
Hasbro is simply required by law to defend its copyright. Which means anything in the same industrial field - animation. Just because they haven't taken down all other fan animated pieces doesn't mean they wouldn't if they were aware of said animated pieces. Hasbro has to prove to copyright firms that it is actively protecting its intellectual property, or else lose its protection for said intellectual property. Fan art, music, etc, likely won't get the brunt of any of this because it's not really competing in the same market, nor can it be viewed as a direct threat to their intellectual property.
That being said, I don't quite understand why this WASN'T protected under fair use. Fan projects are allowed in the world, so long as they are not being used to further financial gains for any party involved (actors, musicians, artists, etc.) without expressed permission from the copyright holder. Which I don't think the Button series was doing, but there may be circumstances that you're not aware of as a third party to this controversy. I'm more surprised they don't go after commissioners of canon content and off brand merchandising, to be honest, as that's actually a direct violation of their copyright by comparison to a not for profit piece. It may be something as simple as claiming fair use, but it may be as complicated as simply needing to contact Hasbro to request fair use.
It is kind of odd, but not all that unusual or wrong. Artists have to protect themselves from the same problems corporations have to. It's not that they're not flattered, but if given a choice between losing your staple or allowing unfettered fan content, what would you do? Their company rests almost entirely on the success of their franchises. If they lose their IP, they're done for.