The foremost being, why was Stoll so crazy? Ithinkthe scene where Stoll atomizes his insufficiently mercenary lieutenant had to originally be later in the movie - 1)Why would Stoll be surprised when the test sheep got atomized, if he already knew and used the technology, and 2) Him going crazy from unshielded pym particles andthenatomizing the lieutenant hangs together logically better. I suspect test audiences didn't hate Stoll early enough, so the scene got moved up.
Then there's the weirdness at the end fight. It _looks_ like there were two different versions of the sequence that got mashed together, with strong suggestions that in one version, Yellowjacket ran out of pym particles and was stuck small until he defeated Ant-Man and took his particles (remember, Ant-Dog is created when Ant-Man throws grow-discs at YJ - why would that matter if YJ could just shrink again; the sole canister of YJ's gold-colored serum is given central prominence in a number of the helicopter scene shots, implying that was supposed to be important), but then all of a sudden he's big and threatening the daughter again.