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