They can be used interchangeably, but there is a slight distinction.
When you have an -ing, it usually means that something is still happening or continuing. It hasn't necessarily ended.
So "He hasn't been feeling very well recently." means he has been sick recently and is STILL sick. But "He hasn't felt very well recently." means he has been sick recently but he might feel better now. It's not definite that he feels better but he might. It all depends on context.
"We haven't spent much time together."
"We haven't been spending much time together." - same as the above, but we are STILL not spending time together.