As it stands, all televised series of Star Trek are considered canon (more on this later). There's an issue that comes up straight away, in the remastered edition of the Original Series. Designs change, along with entirely new ships added. This is an example of adding to the existing canon, while technically breaking the established rules.
Canon is a hard pill to swallow in Star Trek. Including the above reference, there are so many different examples of things changing throughout the franchise. Gene Roddenberry was selective when it came to what was and wasn't locked down lore. He initially didn't count there to be an ongoing continuity between the Original Series and The Next Generation (not to mention the Animated Series), meaning that rules could simply change as he saw fit.
While many examples of canon violations in the early years of Star Trek can be explained away as Roddenberry simply enjoying himself, later canon violations become somewhat harder to explain away if the show is set on keeping continuity.
Looking at you, Star Trek: Discovery.
Let us take a few examples of the times when canon issues have arisen in the course of the franchise.
Writer. Reader. Podcast Host. I'm Seán, I live in Ireland and I'm the poster child for dangerous obsessions with Star Trek. Check out my weekly podcast on all things....well all things film! Check me out on Twitter @seanferrick or at the website https://seanferrick.wordpress.com/