Not so long ago, when I defeated a team rocket grunt, for some reason it gave me 99 balls. Aaaand, my phone died. Did I miss anything? And if so, what?
There’s a glitch where if your Pokemon storage box is full when you beat a grunt and before you go to the catch encounter, the game tells you that you earned 99 premium balls to use. Then you get booted from the catch encounter because your box is full. Make sure you have room for additional Pokemon, and you’ll be awarded the appropriate number of balls.
Ok, that explains a lot
If that happens all you need to do is make room and transfer something, then when you click on the pokestop again you will be able to catch the shadow pokemon.