I think there is a subtle difference between them.
Both are basically compliment for doing good job, but they can be interpreted by context.
Let's just say i'm English learner.
#1. just for compliment
Me: She has a dog.
Teacher: 잘하시네요. or 잘하시는데요.
In this situation, those sentence, 잘하시네요 and 잘하시는데요, can be used for themselves.
#2. if I've done well, but I also have mistake. It's not a big deal, though.
Me: She have a dog.
Teacher: 잘하시는데요. but you can't use have. you should say she has a dog.
I tried to do my best, and my teacher didn't want to make me feel bad. so 잘하시는데요 is an indirect way to say with compliment.
I'm not English native speaker. I hope you feel this answer is helpful, even though my explanation is unpolished.