To answer the question, no it will not affect fish, coral or other inverts. I have accidentally gotten some on some GSP and a hammer with no side affects.
Sadly, if you see three small Aiptasia, there are probably more. I have a 20 gallon coral QT tank that i have been battling Aiptasia in for about 6 months and am finally at the point where I give up. Aiptasia-X is an awesome product for killing the ones you can see, but it is impossible to guarantee you are getting every single Aiptasia in the tank and sump, (or whatever filtration you are using). If you miss one or there is one that you cannot see yet...they will start popping up all over again.
Since this is in my QT tank, I have given up trying to get rid of them completely and just kill them as they appear on the coral racks. I ignore all the ones on the sand bed, rock and glass. As long as they are not close to any coral I just let them be. I just have to make sure I inspect my coral closely, remove the plug and scrape off the coral before dipping and adding to my DT.
I have thought about tearing the tank down and starting from scratch, but since this is a QT tank, the chances of getting Aiptasia again is pretty high so I am just managing it for now and making sure I do not transfer any into my DT.