If you're crushing the berries as part of your process, it releases a resin in the skin that turns green. The best way to minimize the green goo is to freeze the berries, which breaks down the cellular structure of the skins and allows the juice & tannins to escape without crushing.
If you put your freshly picked elderberries in a bucket or bowl of water, the green ones will float, as they are less heavy with sugar than the ripe ones. You might be surprised at the percentage of unripe ones, as I am. I doubt this is what's causing your green color, though. I agree that you should not crush elderberries. Freeze or simmer, or both.
I'm guessing you aren't talking about the "green goo" from elderberries, but rather the camo-green to grey discoloration you sometimes get when adding KMS. If so, know that this color change is transient and harmless.
Yes green goo is real for elderberries. When you rack the wine, be sure to leave it behind. The hard part is getting you fermenter and carboys clean from it. Put a bit of vegetable oil in the water when you wash them and it will dissolve and come out. Then you can use a bit of mild detergent to get rid of the vegetable oil. Be sure to rinse well after the detergent.