Maybe he cried at 3:30 because he had to go to the bathroom.  I take mine out at 10pm, 2am, and 6am.
 
Mine always cried in the crate.  I did the crate at night thing for about 2wks but my husband gets up at 2am to go to work every morning and he'd disturb the puppy so I decided to just put him in bed with me.  It made my life easier.  
