I will preface this comment with I know the reasons why the show is like this, but still bugs me when I watch.

1. The number of issues that could have been prevented by having some kind of protective suit are huge. Isolate from toxins, bacteria, viruses. It would have made for some very short episodes.

2. Having any kind of idea about real security. Every visitor to the ship has almost free reign to go anywhere and do anything. The computer can be accessed by anyone. You can just wander onto the bridge. No lockouts in any equipment, including things that are critical to crew and ship survival.