What difficulty level are you playing? Did you have your whole away team concentrate fire on the medics first?
Did you have to defeat these groups in order to complete the mission? Whenever I can I try to avoid fights that I don't have to get in to. Because 1) ground combat the way it is now is mind numbingly boring and repetitive, 2) using the minimum amount of force necessary is more in line with how Federation officers would do things.
On the surface of planets its easy to go around enemies. They're just standing there and the don't see very far. Inside stations, ships or whatever you can almost always sprint right through them. They usually never chase you outside of the room they're in.
So, if you're finding a group unbeatable and you don't have to kill them. Just move on.