My puppy went away to train for 3 weeks but the trainer says I sill need to work with him. He's seems frightened of everything. What can I do?

I got this puppy in July. He was 3 months when I received him. I work 2 full time jobs therefore,leaving me with little time to train him properly so, I FOUND A TRAINER FOR HIM. HE WAS AWAY FOR THREE WEEKS IN TRAINING. I want to know if that was a good idea. He learned the very basic: sit, stay, down, and recall. The trainer instructed me that I'd need to work with him still. I was under the impression that if I sent him to be trained that this would do it,however the trainer said that my dog was somewhat stubborn and sometimes will not obey the commands that he was taught. My question to you is was this a waste of my hard earned money? I really love my dog and he is a good puppy I just need to know what to do from here? Do you have any suggestions for further training for my pup? And now also since I HAVE HIM BACK HE SEEMS TO BE VERY FRIGHTENED. He seems to be afraid of everything even sometimes his own shadow. Please give me some advice.