The game's title was invented by Craig McCracken, Lauren Faust's husband. During early development shortly after Lauren joined, the team was trying to come up with a name for the new version of their game, and Craig walked past and on a whim, blurted out "Them's Fightin' Herds"! (Which is, of course, a play on the phrase "Them's fightin' words!")
Originally, the Cuddles boss fight was lacking a boss fight theme, and at the time, they had a song just lying around that was going to be used for a cut mini-game in the story mode. The developers took the song intended for the cut mini-game, and put it over the boss fight, and needless to say it fit like a glove, so they used the cut song for the boss fight that it had not even been intended for, but fit really really well.
In early February 2013, Hasbro (the company that owns the rights to the "My Little Pony" IPs) ordered a "Cease and Desist" notice to the developers of this game, "Mane6", resulting in all My Little Pony: Friendship Is Magic (2010) elements being removed from the final game.