Was Applejack in the right for wanting to stop the bats or was Fluttershy right for wanting to find an alternate route? Fans seem split on either option, especially since that plot point was quickly dropped in favor of a potentially better one. Fans are split on that as well, half wanting to see that plot be fully developed while the other would rather they do the Flutterbat plot.
As for the episode itself: was it a funny and weird little romp with a cool transformation, or was it a silly and ridiculous Idiot Plot that seemed ripped from a fanfic?
Informed Wrongness: Applejack. While she agrees with Fluttershy in the end, her initial position, that keeping the bats around risks destroying the farm, is an entirely valid argument. Fluttershy's plan doesn't really address the problem at hand, yet AJ is treated as being in the wrong for not initially going along with it.
Strawman Has a Point: The episode's intended message is that Fluttershy was right and making the vampire fruit bats not eat apples was wrong, but to many the "neutralization" seems like a perfectly harmless compromise that both protects the fruit bats and the orchard. Other viewers argue what would have happened to bats unable to eat their main food source. This is especially controversial when you consider what happened to the Parasprites after Twilight changed their nature; on the one hand, they appeared to be fine afterwards; on the other, they caused a lot more destruction than they would have normally.
They Wasted a Perfectly Good Plot: The episode could have easily focused entirely on the conflict of Applejack wanting to get rid of the vampire fruit bats vs. Fluttershy trying to find a more humane approach to the situation. Yet, given how everyone else pretty much sides with Applejack's idea (not to mention the hand wave to explain where the rest of the Apple Family was during the episode), it feels like "vampire fruit bats invading Sweet Apple Acres" plot point was only there to serve as a set up for turning Fluttershy into a vampire.
Wangst: Fluttershy's constant complaining about using the Stare can come across as such, since she was never shown to be this reluctant about doing so, and as noted above, comparable things have been done in earlier episodes without her batting an eyelid.
What Do You Mean, It's Not Political?: With the debates about the species’ drawbacks and benefits for the farm’s economy, Fluttershy’s communication issues with the bats, and the general rhetoric used in the debate, one could think they were discussing the issue of immigration instead.