Hello snowbull,
We're really sorry to see that you missed a shiny yanma. But, for technical reasons, it's not possible to just make this time lower. Also, you know from being in Safari that you will continue to encounter pokemons as long as you're in the grass, farming for them. If you have your team full, you should have waited to make some empty space before continuing to encounter pokemons.
Unfortunately, we cannot refund anything about that nor repop the poke you missed, because you missed it due to not leaving you a free slot in case you encounter a really good/rare/shiny pokemon :)
We hope that next time you will spare a slot and try to not encounter some more pokemons if you cannot capture any :D
I'll now lock this topic as solved.