You may need to leave him in the crate unless you are really watching him closely. WHen he's out, he gets busy and does not notice his body's signals. And when he is in the crate, he does not want to soil his den. He will get there. You just need patience, which I know is hard to come by, especially when you are lacking sleep from getting up with him. The baby stage does not last long--it just seems like it at the time!
That's absolutely normal at that age. He probably whines in his crate because it's unnatural for a dog to go potty where he sleeps. If you are consistent, he will catch on eventually. My boy was easy to potty train, but he still had the occasional accident until he was about 6 months old. He too needed to go outside in the middle of the night until he was about 4 months old. Dogs like children are different, so just keep up the good work.
