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Its pretty easy to not see something in a reef tank until it's been setup several months. I just found out I had a porcelin crab, and my tank was started the first week of July 2004.
That's what I've loved about my SW tank. It's been up over a year and I can still find things I didn't know I had! And it's only a 55.
Regarding the "jelly fish" Most jelly fish are "bad for you" anywhere from a bad sting to sudden death. However, it's highly unlikely you have the sudden death variety in your aquarium as they're rather large. Actual jelly fish will always be suspended in the water column, I don't think there are any that will "rest" or settle on the substrate/rock. If what you saw was on a rock or the glass, i doubt it is actually a jelly fish.
Try taking a snapshot of it so we can help you identify it. (and you might want to post the pic in our Identification Forum) just post a link to that thread in here when you do!
I think many do that. I get some really nice "Florida" acu-cultured LR from my fish store. It is exactly like the keys from liverocks.com. However, when you buy it, they inspect it for any hitchikers and take them off. "Why give a way what you can sell???" is the response I got.