In a plastic bag does not mean they've been grown emmersed; most likely they were just bagged that way for convenience. The bag maintains humidity which allows the plant to survive. Hence your fern should adapt just fine.
As for your algae problems, I think you've to provide more information like your lights and dosing regime. It is typically imbalances in your tank that cause it.
When I spot dose it normally doesn't kill my plants. Perhaps you injected too much? Especially since java fern is a tough plant.
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