When traveling on auto-pilot to another sector block, passing near the entrance to another sector block while en-route will cause the bridge officer pop-up asking if you would like to warp to that sector (which stops your ship, extremely annoying if traveling at Slipstream as it wastes some of your slipstream time).
Since the game seems to know when your ship is on auto-pilot (the ship will change speed and direction to avoid obstacles), it would be nice to have an option to suppress these pop-ups and instead just show the buttons at the side of the user interface that appear after you have dismissed the pop-up. For example, if leaving the Sol system and setting a course for the Beta Ursae sector block, it would be nice not to be interrupted by the option to warp to Delta Volanis and rather just have the button to warp to Delta Volanis appear at the left, since the game should be able to figure out that Delta Volanis isn't where the player is heading, as the auto-pilot is already set for Beta Ursae.
Another thing I've noticed is that while leaving an exploration cluster will usually place you back in the adjacent sector block facing away from the exploration cluster, a few will place you in the sector facing the sector block that you just came from. This has the annoying side affect of causing the bridge officer pop-up to appear as soon as you set a course and start to move.
I think a little extra logic to avoid these pop-ups while traveling on auto-pilot would be a really nice quality of life feature for the game.