sbutts,
You don't have to remove the Aiptasia when treating with Aiptasia X. What happens when treated correctly is the Aiptasia will consume the product and it's oral disc, or mouth will be closed up by the glue like effect of the product, and then the Aiptasia literally implodes and melts away over time. The sealing of the mouth keeps it from spewing out any larva into the water column that could later spread. Now let me state what I mean when I say "treated correctly" the Aiptasia have to eat the product, or it has to seal there mouth. If it only lands on them or scares them into hiding, it will not work. An Aiptasia is an anemone and you have to realize what you see is only the top of there body, the base is often hidden deep in the rock your treating, and if they retract in, all that happens is the product irritates them, and a few days to a week later there back. However if they eat it or it seals there oral disc, there done for and gone for good.
Most likely when you treated the Aiptasia it only landed on it, and in defence it pulled in or retracted, and once the product was washed off it's body it was able to come out of hiding.
I've used this product for years with no adverse affect to corals or fish, and some of my fish have even eaten it, which I don't like, but it has happened. And everyone stays in perfect health. I've had it land on a few corals now and then as well, and while the coral may retract for a day or two it comes back without any problems. It can be a tricky product to use at times however I will say it's the best I've found. Treating large, reachable, easy to see, Aiptasia with Aiptasia X is simple, it's treating the small ones or hard to reach ones that's a real pain. This is why I personally also have a few Peppermint Shrimp as well, although even these guys are no guarantee. They normally will loose interest in Aiptasia when presented with another food source.
Best tips I can give you when using Aiptasia X:
Turn off all pumps during treatment, and I normally leave mine off for at least 30min after treating as well.
Go slowly, you don't want to scare them into hiding.
Make sure the syringe is working smoothly, sometimes it will stick and it causes a large amount of the product squirt out. Which normally just scares the Aiptasia.
If your treating one that's hard or impossible to reach with the small syringe, try to length the tube. (what I did was used an old plastic RC antenna, slide it over the needle with a dab of super glue to hold it in place, and you now have a 12" needle)
Check your sump and overflow box for Aiptasia as well.
Watch this video too...
http://www.redseafish.com/show_movie.asp?product=296&type=high