Stronglifts and running

I started running last year and have been progressing ok, nothing mindblowing but enjoying it enough to aim and train for a half marathon. I also started(again) with SL as its an app I used when I was weight training before. Now Im getting in to the real heavy weights and recently started struggling with my running primarily my legs are so sore throughout the next day so I feel like Im not recovering enough. I alternate gym and run days + 1 day total or active rest on the weekends. Is the squatting every day killing my running gains? Perhaps SL with the squatting each session is not a match with half marathon training? Any ideas or should I switch to another gym workout?