It's a problem with the drafting – the original authors always meant for there to be exceptions, but decided not to specify explicitly in the text what those exceptions were going to be – thus leaving it up to the courts to decide in practice what exceptions are allowed and what are not.

The obscenity exception was largely non-controversial until the 20th century, because there was a broad societal consensus, among both popular and elite opinion, that obscenity and pornography did not deserve First Amendment protection. It was only in the 20th century that societal consensus broke down, and it was in that context the US Supreme Court decided to reduce the scope of that exception. (It still exists, and is still occasionally enforced.) The original authors and ratifiers of the First Amendment supported laws against obscenity, and didn't believe the First Amendment prohibited them.

Ultimately the courts have to decide what laws mean, even constitutional laws – but they could always have given them more guidance, by being more explicit in the text about which exceptions are valid and which are not