On my first playthrough, I actually wasn't able to break the crates at all. In fact, I coudn't break the crate at the top left of the beginning of the stage as well. It had me really puzzled on why I can't proceed with the game until I restarted and found out that I can break those crates.
Strange things happen when you restart (maybe it's got something to do with me losing focus on the game's window on the first time I ran the game).