I've recently downloaded Pokemon go and I've caught a few but they only show when I caught them in my journal and not in the Pokemon folder where it names all the Pokemon that you've caught why is this???
Back when your question was asked there were a lot of communication errors and server errors. These have since been resolved.
I too have seen this happen to me once or twice. And I've seen it happen on other people's phones too. This was a communication error with the server. The Pokemon are there, just not displayed.