The lost of certain plant or animal species can have horrible effects on a ecosystem and the same can be said an introduction of either two.
So what happens when the flora and fauna of Earth ends up in Equestria?
The same thing that happens here on Earth, an inbalance of the ecosystem. Only difference is that Earth's ecosystem can balance itself back naturally but on Equestria, the inhabitants have to do it themselves.
Consider some of the horrifying things that Mother Nature has come up with and you can see where this is going.