I slow down to some very low velocity when I get at about 7 km and slowly, slowly approach them, to stop completely when I am at the scanning range. Sometimes it helps. But mostly I just get frustrated and wait for others to scan them and then I just focus on the second part of the mission.
I approach under cloak, park at 0km, and decloak only as long as the cloak cooldown requires so I can scan it. It's the only way I can avoid getting shot in the @ss and killified by some Klingon gank squad.
The mark showing the distance is not the centre of the object, but the top left of the bracket that is highlighting the object. As most objects are small, it's easy to get into the habit of thinking that the top left part IS the object.
Because of the size of the objects in question, you can easily miss the bottom right corner so it looks like the top left is the normal thing you'd fly towards.
Try zooming out and panning downwards to see if you can see the bottom right. Once you do, you'll see the actual object you are aiming at. Just remember what it looks like and aim for that instead of the distance marker and you'll be fine