Those pattern buffer filters aren't getting any better over the decades, are they?
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.
The problem with Star Trek is, and always has been, that writers keep making it harder every episode for later authors to find ways of introducing crisis like these. Every solution closes a plot device door.
Star Trek has a serious Eagles Flying The Ring To Mt Doom problem.