Crate training is awesome to use for when you’re not home and want to maintain the house and not only that but not have to worry about your pet getting hurt out of being curious running around the apartment or house and knocking over something that may hurt him or her.
From the little I know though the question of if there are negative outcomes to using crate training, it would depend on the person training their dog.
Some people will be hard on their pet for not picking up the training techniques fast enough and other people take the time to teach their pets that using the crate is their mini oasis.
Either way all of what I have to say is opinions but I did do a bit of researching into what you asked and found an article that talks a lot more on this.
Check it out when you have time Ace: http://allibarrarabians.com/no-brainer-guide-crate-training-puppy/