Quite a few times.
May I get some examples?
According to "The Alternative Factor", if a single particle of antimatter were to meet a particle of matter, then "everything, everywhere" would be destroyed. Wind back to "The Naked Time" and a matter/antimatter reaction is what powers the Enterprise's (and other Federation starships') warp engines.
Then there's the dupicate Earth's the Enterprise encounters. They go from being an amazing once-in-a-lifetime discovery to mundane then back to amazing again.
The era Star Trek is set in fluctuates between 200 years in the future ("Space Seed") and 900 years in the future ("The Squire of Gothos")
Fleet Captain Pike is "about [Kirk's] age" according to Commodore Mendez in "The Minagerie" yet he commanded the Enterprise 13 years prior, and Spock served with him for 11 years. That means Pike became captain age 9.
If you include the TOS movies.... why does everything look totally different in The Motion Picture? Does Vulcan have a moon? Why are Khans followers suddenly all blone haired? Do Klingons take prisoners? How old is the Enterprise? Do they use money in the 23rd century?
...and so on...