I'm curious if there is a way to Annex States that are one state, allied, and in your sphere?
I accidentally sphere Krakow as Germany and now I have alittle nation in the middle of my country and I cant get it out of my sphere to take it by force nor can I find a way to anex it otherwise?
No. There is no way, unless you are a Cultural Union country and they are part of your cultural union (for example, Germany annexing an independent and sphered Bavaria).
If you sphere a country, you cannot attack it, as you certainly noticed. So keep in mind: Only sphere countries you don't plan on annexing/attacking later. If a sphered country is a secondary power with low relations towards the sphere leader, they may get an option to leave your sphere, and the sphere leader would get an event with a CB against them.
Why is it, that my population in Two Sicilies constantly falls? I've tried lowering taxes, encouraging the poor, all sorts - even as a Great Power my population just isn't growing. After Annexing Tunisia I have 2.2m, up from 1.8m - it's now about 5years later and I'm back down to 1.9m! Any ideas / input greatly appreciated
The cause is probably emigration due to high consciousness. This thread might be useful.