There are at least three parts to this. One is the science. The science should have initially been saying "We don't know", and then "We think X, because Y, with Z level of certainty", with Z getting more and more certain as time went on.
Second is the public health aspects of this. They had to say "Do U, V, and W" before the science was clear that those were the correct things to do. (Why "had to"? Because if they said "We can't tell you what to do", first there would have been panic, and second they would have missed a chance to get ahead of it if they guessed right. So they went with their best guess, which is not an unreasonable thing to do.)
But the third thing is politics and reputation. They went with their best guess, but they didn't admit that it was a guess. They wanted everyone to do it, and so they talked like they were certain, even though they didn't have the data to be certain. When some of their guesses were wrong, they took a reputational hit, because they had sounded like they were certain. Then, compounding the problem, even after the evidence started to come in they stuck to their original advice to try to avoid taking the damage to their reputation, and just wound up making themselves look like buffoons. They damaged the reputation of public health for decades by how they handled this.
Second is the public health aspects of this. They had to say "Do U, V, and W" before the science was clear that those were the correct things to do. (Why "had to"? Because if they said "We can't tell you what to do", first there would have been panic, and second they would have missed a chance to get ahead of it if they guessed right. So they went with their best guess, which is not an unreasonable thing to do.)
But the third thing is politics and reputation. They went with their best guess, but they didn't admit that it was a guess. They wanted everyone to do it, and so they talked like they were certain, even though they didn't have the data to be certain. When some of their guesses were wrong, they took a reputational hit, because they had sounded like they were certain. Then, compounding the problem, even after the evidence started to come in they stuck to their original advice to try to avoid taking the damage to their reputation, and just wound up making themselves look like buffoons. They damaged the reputation of public health for decades by how they handled this.