When you drag a layer beneath another or in-between two, the layers will get swapped. This makes it difficult to organize layers when you have a lot of them.
As you add more layers and want them in-between, the problem grows.
The layers are swapped, putting layer 2.5 at 2 spot and 2 and 2.5 spot.
The layer is moved between 2 and 3
Example: move 2.5 between 2 and 3:

Follow the gif above:
This will definitely be fixed in #533.
@scribblemaniac @CandyFace This is related to this issue #436 which was brought up by JonasThomas he even did a video where he explained this and other stuff. https://www.youtube.com/watch?v=INAsUcpywL8&feature=youtu.be He did fix a few other problems around that issues, but this particular layer behavior got stuck. Could be worth taking a look at all that thread to understand what was implemented too.
This issue should be closed. Fixed long ago.
@davidlamhauge You're right. This was fixed by #1147
Closing.
Most helpful comment
This will definitely be fixed in #533.