Online check-in systems often simply don't work as well as they are supposed to. I fly very often from Europe to the US, and my success rate on checking-in online is maybe about 60 %. It highly depends on what airline you are flying as well. I even called an airline at some point, and they confirmed that I cannot check-in online, but couldn't tell me why. It is not necessarily related to a second screening, though there is a non-vanishing probability that you cannot check-in because the system volunteered you to be screened.
Usually, once you are at the airport, all these problems go away. It's still a nuisance for you, since you have to go to the airport earlier if you cannot check-in online. And nowadays there are only very few check-in desks open, since everybody can check-in online... well, in principle at least.
I once even made it to the US border without a valid ESTA. They allowed me to apply for an ESTA while at immigration. I do not suggest to try this, though!