MLP:FiM Season 9, Episode 18 - "She Talks To Angel"

[Al-1701]

And of course Fluttershy doesn't regret having any pens or barricades to separate hostile animals.  Oh no.  That would be cruel.  Far more cruel than having a baby elephant left defenseless against a snake strangely obsessed with eating them.

Dr. Fauna should be able to handle things like any other vet.  They can't translate animal communication to language, but they understand behavior well enough.  Though, this is Equestria where everyone beyond the Mane 6 is helpless in order to justify their importance.

[TJgamer]

I can sort of see where you're coming from with Dr. Fauna (the vet). She probably could have contributed a little more, but bear in mind she can't do what Fluttershy does exactly. What would you want her to do exactly?

The vials reacted differently? Different formulas? What do you mean? 

:Well as a vet, she didn't really do anything to control the situation with the animals. As for the vials, they affected Fluttershy and Angel differently. They just switched bodies without explanation.

One of her potions also allowed Twilight to see into the past without explanation.
Best way I can explain is that if the same liquid is drunk by two separate living beings (who I guess are in close proximity with eachother), they will switch bodies.
It's magic mumbo jumbo.