Kerbal Space Program

Saw this is 1.11.2 too, even without timewarping they were glitching..

This has kind of been the case for a long time. I've always blamed it on rounding errors that develop during the warp much like how the physics gets changed and things like fuel harvesting and power consumption don't match up with how they would at real time speed. It seems like they have to convert to smaller bit-sized numbers for faster visual calculations during a warp but it usually goes back after you drop out. I often jump up to just one warp arrow (5x) manually before using the warp to maneuver as an example. This helps me to see if something is going to jump way out of place first before I make the problem worse as some of these do result in permanent changes (also a bug). I'm really hoping KSP2 does a better job with all of this.

Doesnt happen in 1.11

Happens in 1.12.3.3173 too, I found this bug to be repeatable. https://i.imgur.com/xA40wCp.png

As someone else said, the intersect markers glitch even when you aren't timewarping. I was trying to rendezvous with a ship, and even though my predicted trajectory from a maneuver node clearly brought my ship close to another ship (which I could tell because the intersects kind of worked), when I modified the maneuver node to bring the intersect closer to the target ship, the intersect node started glitching out and showing a different intersect other than the obvious closest (closest in time and distance) intersect. I think this is a pretty severe issue and it's still present.

Intercepts/encounters decreased in accuracy in 1.8 for some reason.
Possibly someone who didn't understand how the code worked and replaced it with something inferior or more simple. Not sure why