I honestly don’t see these problems with canon that you are seeing. But I’ve realized some time ago that in general fandom basically seems to break up into two groups:
- One that looks at Star Trek as a collection of distinct TV shows that just happen to be taking place in the same, loosely connected fictional universe, each one kinda telling its own stories, with its own flavor and unique take on the Trek sandbox.
- And the other one that sees Star Trek as en epic, continuous tale, where each show adds to a larger narrative about, I don’t know, the “History of the Federation”, or something like that.
I think both viewpoints are valid, but I find myself in the first group. I appreciate if something ties together neatly from one show to the other, but it’s not what
Star Trek “is about” for me.
And I guess it’s largely the second group that tends to obsess over continuity problems, “breaking canon” or filling in blanks.