Noticed when catching new Pokemon, played with boxes for a while to confirm

 

1) All new Pokemon are being stored in box 1. This is on top of the already (seemingly) full box. These Pokemon are find-able with the search function only

 

2) Taking Pokemon out of box 1 will relocate Pokemon from other boxes into box 1

 

Steps

I placed 2 Pokemon into box 3

I took out 2 Pokemon from box 1 and tried to put them in box 14. They both disappeared

Searching for them by name, they were still there

Box 3 Pokemon had also disappeared, and were now in Box 2

Removing any Pokemon from box 1 into party also moved 1 Pokemon from Boxes greater than 1 to Box 1

 

As a result I could not relocate Pokemon from the overflowed box 1 into other boxes because every time I pulled a Pokemon out from box 1 it would be replaced with a Pokemon from one of the other boxes

 

I restarted the game to confirm glitch still present

 

All Pokemon are stored in box 1 except for those of the party of 6

 

Sidenote: For Pokemon "lost" in the PC i have been able to find them by searching by exact name

The pokemon that store in PC are not same with original game, it's not store in BOX by BOX, when you put a new pokemon into it,it automatically put into the last available position. So, it will go to the last position of the last filled box, when you take out a pokemon from it, the original place will replace by the next one.

 

Unless you replace the Pokemon in your team with a pokemon from box, then their place will swap.(Do by holding a Pokemon from box and place it on top of a pokemon in your team)

 

It's not a bug, but the designation of the PC storage system. And your so called "missing pokemon" , actually they are in the last position of the last filled box.