Oh, there are hundreds of thousands of little transgressions. Janeway only caused a recursion a few decades long, and only for one ship. Those get cleaned up by Daniels and his band of merry time police.
But these two major crossroad events in particular created such strong branches that Temporal just had to massage it as much as they could and live with the functional damage.
Bare in mind, The Janeway also disrupts the Prime Timeline before both First Contact and Kelvin.
Oh, there are hundreds of thousands of little transgressions. Janeway only caused a recursion a few decades long, and only for one ship. Those get cleaned up by Daniels and his band of merry time police.
But these two major crossroad events in particular created such strong branches that Temporal just had to massage it as much as they could and live with the functional damage.
Red Matter: Not even once.