I thought my legs were getting better after resting them for a couple of days and doing some gentle stretches. I didn't want to start losing fitness so I went for W3R1. Breathing wise, everything was fine and I managed to finish the run. Unfortunately it did make my legs more painful. So frustrated. I will take another couple of days off and see how they feel.
W3R1: I thought my legs were getting better... - Couch to 5K
W3R1
It could just be because you're a new runner and your body is getting used to the exercise. I see from your previous post that the pain is behind your knees. This could be tight hamstrings (back of your thighs). Make sure you stretch this area well and maybe take extra days off before you try again.
I think IP is right. Your body is just getting used to it. I have a plastic roller from amazon which I run over my thigh and calf muscles before and after each run. That helps and I take a bath with Epsom salts once a week which is good for general aches and pains and a good way for the body to absorb magnesium. It will get better but muscles do complain when they are asked to do things they aren't used to doing. Are you doing any stretching at all after your runs?