This is a very old bug. As far as I can tell, it was originally reported on Multiverse's Github here, then later brought up again here.

This bug is not obvious in a vanilla Spigot server, because it has only one Overworld, and time does not matter in the Nether or the End. However, it is still demonstrably present. Setting the time in the Overworld also affects the time in the Nether and End. These steps show this:

1. Set the time in the Overworld to 1000 using "/time set 1000"
2. Go into the Nether
3. Observe that the time is close to 1000 using "/time query daytime"
4. Set the time to 0
5. Go back to the Overworld, and observe that it is now near 0

This is an annoyance on my server that uses Multiverse, and has multiple overworlds. There, night and day are meaningfully different, and we would like to be able to lock one world on day (a creative world), while keeping another in the normal cycle (a survival world). Currently, if one player sleeps in the survival world, this often changes the time in the creative world to night.

This is not a huge problem, but seeing that it has been a bug for almost a decade now, I am hoping we can get this resolved.