1. I've never used a crate to housetrain.
2. I have, apart from one puppy we bought (more later), always found that if a puppy is taken out often enough so there's no need to be messing in his crate (and fact is apart from overnight, our puppies weren't shut in a crate other than if we needed to do other things (go out) to keep them safe and out of mischief), eventually they learnt there was no need to be messing in their crates - they learnt to hold. Provided they could, physically.
3. I also don't believe in confining a puppy to a small area in a crate (we bought the size needed for an adult) because if they needed to empty, and before they'd learnt to hold, or could, they'd just empty in there, and be forced to lie in it if the space was small - nasty!
We had one we bought in, after many years with our home-breds, who from day one was peeing for England. She was 8 weeks but clearly there was something very wrong with her. A Ph check of her urine showed she did have a problem and she was put on antibiotics - no change. My then vet started talking about 'bladder stones'. Hum. I took her back to her breeder, hoping she'd get her sorted out and let me have her back. She took exception, slapped a refund cheque at me and that was that. She later said all her remaining puppies in that litter were 'the same' according to her vet. Whether this was a weak bladder I don't know but her Ph was wrong. Interestingly I noted from the KCSB Records, that the poor girl went to 2 more homes after mine before she apparently settled.
So if this is going on, I'd rule out some medical problem (urinalysis) and then just keep doing what you are doing and hope he catches on re not messing in his crate. With mine, as puppies, I'd put them in their crate last thing, after being taken out to empty, at around 11 pm and then get up around 3 am for an outing and then up for the day by 7 am. Not all puppies are the same, as I discovered!
And yes, have his crate alongside your bed so you will know when he's restless and can react. I tried to anticipate them stirring so they didn't think they cried, you came.