OK guys, it happened again just now and I've got it on video. The situation:
I'm going out on a bounty. I plot the course and it's only one jump:
View attachment 306196
Here's the jump range right before I hit the button:
View attachment 306199
Here's my Krait Mk II's range:
View attachment 306202
Here's the video of what happens - I set the course, go back to the cockpit, aim at the destination, hit the button to power up the FSD and the destination instantly vanishes and is replaced by a destination on the opposite side of the environment going the other way. This is the issue I was having that was driving me nuts when it suddenly quit doing it. Now, it's back.
Source: https://www.youtube.com/watch?v=pOfNGo5_-3E
You have a scanned wake targeted. When you initiate a jump with a scanned wake targeted, it will attempt to jump to that system similarly to as if that system was directly targeted (like you would through the galaxy map or the navigation panel on your left). Like described in message #39, targeted objects/systems take priority over the route.
Plotting a route clears navigation locks (such as for planetary bodies, stations, or other systems), however, a wake is a temporary, targetable object within local space, and those stay targeted even if you plot a route. So basically, it's a dev oversight not having implemented a "clear target" command simultaneously with plotting as it does with navigation locks already, for this one edge case where a locally targeted object can alter the jump behavior.
Use a bind to change your target (such as "select target ahead", default "T" on keyboard) to deselect the wake before initiating the FSD sequence and it'll jump to the plotted route you intended.
The reason why wakes do this in the first place is because they're meant to be a tool for chasing ships that have succesfully fled a pursuer (hostile or otherwise), and as such, it wouldn't make sense to have to find the system and manually target/plot it after you've found out the system the ship jumped to when it's usually a time-sensitive situation. The material gathering mechanics for engineering were only added a few years after release and prior to that, the sole purpose of the wake scanner was for such scenarios.
If you raise a ticket in the issues tracker, you might be able to get it fixed so that such a situation doesn't happen to you or anybody else, but this is in the realm of where it could be written off as game mechanics just working in a unique, if negative, way, so I doubt it would be seriously considered to be changed.