Could you list where and when the offending events happen? Or at least as many as you can recall? Neither myself nor LaZ can remember where they are, so you would be helping to get it fixed if you could list as many as possible.
I second this question. It could simply be that you're trying to grind - which the new levelling system discourages by giving diminishing returns.
A leftover from copying the decapped names over from the 649 Patch. The script is supposed to prevent you from battling these Pokémon, but apparently it's not working as intended.
You get the Solar Rock at Level 10, I believe. There is a bug however, where you get stuck permanently in the Cave of Wisdom if you save after starting. We're working on this bug at the moment.