sound like the crate wasnt properly introduced, I myself would never put my dog in a crate or lock him in a room , with propper training a dog can be left alone by himself with the run of a entire house and not do any damage. my puppy is 5 months old, he lives in my downstairs bedroom which backs onto the garden , the kitchen and the front room. when we go out we simply close the baby gate off from the upstairs of the house and he is free to run free. Unless we have been stupid and left tissues on the floor everything will be in tact when we come home. This has been a very quick process, He was very well behaved before we took him to puppy classes, he could already sit, stay, come when called, and responded really well to the word "No!" you have to say it firm enough so he knows you mean business - depending on the breed dont be scared of frightening the little thing, he needs to know your boss. The crate should have been introduced as a safe place for him, you should have let him investigate it himself initially, add toys and blankets that have your smell on them or his own smell, then after a few days- occasionally shut the door, go out of sight for no more that 5 minutes then return only when he has stopped crying for you. praise him with a treat , and repeat it every so often this way there is no chance of seperation anxiety. Maybe change the room , and definatley give him some natural light. maybe no noise of a fan, crack open a window, try leaving a radio on, I have always done this with my dogs I think they feel like they are not alone in the house if they can hear human voices whilst your out. I am not sure how to rectify it now, I would go and see a professional- local obiedience classes. One more thing, dont expect your dog to misbehave when you put him in his crate- he can sense this nervousness. How long is he left alone for......... And if he is not in the house alone , why is he in a locked dark room?
GOOD LUCK