Those pattern buffer filters aren’t getting any better over the decades, are they?

To be fair, they are designed to work with all kinds of species, and samples and things. You don't want it to delete someone's liver just because they haven't been on a starship before, or the new plant sample taken from a new planet.

Humans are full of necessary bacteria, and deleting all of that would be quite bad for you. But at the same time, them being in some place they're not supposed to be is also going to cause problems.

You know, they should not even let the doors on shuttle craft open in dock, and just beam people in and out of them. That’d solve an entire other vector of infection.

What's more surprising is that they don't employ the sterilisation/quarantine fields that the older model transporters used to have, where they'd wall off the transport pad, blast them, and then open it up. That doesn't seem unreasonable to apply to a shuttle before landing.