Another Egglocke Issue

Another problem in the same save file, Pokemon Insurgence Light version with female trainer Rose...

Every time I catch a Pokemon, it isn't swapped out for a Pokemon Egg from my box. I randomized 20 boxes of eggs but I am only on the Egglocke Challenge, no others. Here is a picture of my party.

So I'm stuck with one Pokemon and Egg tokens I can't trade for Eggs. I think I'll restart my game.