This has happened to me 3 time, and all three times, it has occured around luna, but after deactivating the automatic burn feature, the planed burn will not go away.
what I mean by this is I can delete the waypoint, then another will appear a few degrees further into my current orbit.
in my screenshots I uploaded, the first screenshot is me the first waypoint. the second screenshot is after I have selected the delete waypoint "x" button, and a new waypoint has appeared
this issue does not persist after a quick save and quick load.
here are some steps that I followed in my own testing to replicate this issue:
1: get into a hyperbolic orbit around Luna
2: set up a planned burn to achieve capture (in my testing, I had the apolune rather high where it was just enough to become captured).
3: approximately halfway through the automated execution of the planned burn, deselect the auto burn button, and complete the scheduled burn manually (this is the most critical step and where I believe the game is messing up).
4: after completing all of these steps, try and remove the planed burn waypoint that you have just completed and passed by. In my testing, this is how I replicated this issue.
note- I tried a similar process in an elliptical orbit while around the earth after setting up a planned burn to raise my orbit with no results of this issue. I have only been able to replicate this issue while around Luna.
I wish I could take a video to show this issue, but I currently don't have any screen capture software on my pc at the moment.