I was able to successfully create an animated gif of the problem. You can see in the gif that they are performing collision avoidance with the pickup rail, before getting close enough to dock.

I tried to stick the pickup point/rails outside of the ship's bounding box like @lancake suggested. Didn't work... Changing the orientation of the docked on the drone also doesn't make a difference FYI.

So it doesn't have to do anything with the ship's bounding box. It REALLY looks like it's just trying to (stupidly) avoid colliding with the pickup point:
https://www.youtube.com/watch?v=6qc3bIMKV80

If your drones are docking backwards, then putting the rail docker on the very back end of the drone, with nothing sticking out past it, might help. That way the rail docker gets in range of the docking point before the drones collision box does.

You can also change your fleet to idle mode just before your drones reach the docking points and they will drift into position.

In T1232#47124, @Kingofanime wrote:

If your drones are docking backwards, then putting the rail docker on the very back end of the drone, with nothing sticking out past it, might help. That way the rail docker gets in range of the docking point before the drones collision box does.
You can also change your fleet to idle mode just before your drones reach the docking points and they will drift into position.

I wish I could do that, but the way I have it set up inside doesn't allow me to stick the docker at the back of the drone. And I'm not about do to change a rail system that took me multiple hours to make just because of a bug :P

Thanks for the tip though, I'll keep that in mind next time.

Now that I look more closely at this task, it seems to be a duplicate of T1238 (or T1238 is a duplicate of T1232). The other task got fixed however ,and after trying this one again, it seems completely fine.

Not sure if you still check this task but can you confirm that the drones are not trying to avoid collision with the non physical rails?

This issue was fixed for me in the last patch release.

Can also confirm that the issue was fixed in the last patch. This bug report was made before the last patch.

Thanks for the quick replies! I'll reject it as a duplicate of T1238