On Jefferson's play to tie the game, I agree that he might have not really had full control right away. But also, at least one or two of those steps were a result of contact from the defender. It wasn't a ton, but it would have been pretty frustrating if they had called a travel because the defender bumped into him trying to poke the ball away.
For the clock, what's funny to me is that the only reason that time was added was because Tech called a timeout to set their defense up. I think that was a poor decision anyway because it allowed Iowa State to draw something up, but it became doubly stupid when the referees went to add time. Then in OT, for the same situation, Iowa State didn't call a timeout following Jefferson's free throws, so the refs didn't look back at the clock and Tech couldn't draw anything up (though they got a good look anyway).