I'm experiencing the same bug! I'm stuck in the pit when I'm supposed to get a balloon and go find the Aether Injector in the Business District. However, there are NO BALLOONS left in the crate because it gave me 2 balloons when I went to get the fog injector. Yes, I still have the second balloon. I mention it just in case it is part of the glitch. We have 2 accounts stuck and I'm expecting a third to get there in the next few days.