Fuse your pins up to Delta, wait until you have 4, and then fuse them all into Zeta. Use Zeta in The Noob formation with the other slots as tanks in order to clear Area 2.
There seems to be a bug with passive skill experience. the skill doesn't level up unless the skill is actively being trained, and leftover experience doesn't carry on to the next level.
Crypt charges should go back to their tower when all targets are destroyed instead of just disappearing. I've lost up to a dozen charges at a time that way.
Don't worry. I'm constantly adding new bugs and glitches just as broken.