Puppies don't lump together peeing and pooping as the same sort of function, maybe because they use pee to mark their territory, but it's not uncommon at all for them to "get" that you want them to pee outside before they get the pooping thing down, or visa versa.
Housebreaking problems can go on for months (even years) if people aren't willing or able to spend some concentrated time for a few days or a week to take care of it once and for all. It can be three or four days of misery...but it's worth it. I once spent five days holding a leash with a puppy at the end of it, watching his every move. It was incredibly boring but he had been "mistrained" for some time before his owners asked me for help and really just needed instant and consistent guidance before he understood what was wanted.
You could start out by putting him on a feeding schedule so you know in advance when he's going to want to poop. No food after early evening so he can make it through the night comfortably. (he shouldn't have to poop first thing in the morning). He can have water up until an hour before being crated as long as he's taken out to pee before being put in.
If you crate him during the day, then make sure he has enough time beween his last meal and his crate time to digest and eliminate before he goes in. If he's reluctant when you first take him outside, give him a brisk little walk, exercise often gets things moving...so to speak.
If it's possible, depending on the weather where you are and your schedule, you could speed things up if you can try to spend an entire day or two outside with him. Get your yard work done, putter in your garden, or grab a lawn chair and a book. If you have him outside all day, he will have to soil eventually and when he does, you will be right there to lavish praise on him...each time he does it.
Make sure his crate is kept squeaky clean. Don't let him remain in a soiled crate once you notice it. You want him to stop feeling comfortable in a soiled crate, so minimize his opportunities to get used to it while building his comfort in a fresh clean crate.
Basically...there is no sure fire method to housetrain except attention. You have to watch them all the time, and if you can't then you need to know when they will have to go so that you can make sure they are in the appropriate place for it at the right time.
Never scold a puppy for getting it wrong beyond a firm "not here" or "no" *when he's doing it* while you scoop him up and hurry him outside. If you don't catch him in the act, it's a freebie. One of the biggest mistakes people make is yelling at their dogs so the dog thinks you don't want him to do it *in front of you*. So he goes behind the couch or under the bed or waits til you're not looking making it much much harder to correct him when he needs it.
Aside from constant vigilance, the biggest thing I think will help you is working out a feeding schedule that won't leave him needed to go during the time he's crated. | 
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