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In "The Man From The Other Side" Fringe season 2 episode, 3 shape-shifter embryos appear in a warehouse. Later in the same episode, they made a quite complicated attempt to pass someone to this universe.
So, how do the shape-shifter passed to ours universe so "easily"?
The shapeshifters came over because they are easier to send Over Here (i.e. the parallel world where our main characters exist). They were designed and built by
William Bell and Walternate
to survive the trip and then infiltrate Over Here's population. We never see the exact mechanism used to send them Over Here, but it must be trivial compared to the steps you need to take to safely send a human across. And that's part of the reason why they're used as agents in the war, because of that ease of deployment.
