On this subject, I did notice that I had a game where a pioneer sent out to a crystal shard only gave half a crystal, and even after many many turns I did not gain any crystals at the top of the screen, nor was I able to cast spells dependent on that crystal. Once I sent a second pioneer to that crystal after reading this post, I got a total of one crystal, and was able to cast spells. I thought maybe this was intentional and seemed to indicate that some resources required more than one pioneer sent out to fully take advantage of the potential of the site.
If this wasn't intentional, then the half a crystal thing needs to be looked into because especially on a small map like the one in the current beta that only has one of each crystal, it makes it flat out impossible to get any benefit from using pioneers to harvest a crysta.
Yea I know that's how I first discovered the bug, spell crystals. I too thought it might of been intentional until I tested it on an Iron mine and just kept sending Pioneer after Pioneer to the same mine then I knew it had to be bug. As for the 1/2 Crystal thing I think that is a balance issue but in general I think pioneers should not have any penalty especially since cities are gonna supposedly have production bonuses as they level up.
I need to see if they really did fixed this in 0.3 which haven't really been able to cause it seems to CTD a bit more then before. And not load saved games. 
Plus I have been too busy writing up long post and catching up on other threads. 