I've been doing BB back squats approximately 3 times in the last 3 weeks. Before this, I've never done any kind of BB squats - period. I've noticed I've been having some discomfort on the upper part of my leg when I descend. The discomfort is there now when I do a weighted or unweighted squat just before I hit parallel. I didn't have this problem when I was doing squats with dumbells, but I imagine I'm working out some different muscles. Also something else to consider, is that I've only been working out since October.

I can't explain what it feels like really, but it's discomforting to both legs in one particular area. I dont know which muscle it is, but like I said it's the top part of my legs -- if I had to guess I would say the it could be the pectineus muscle, but I'm not qualified to make that assertion. For all I know, it could be the rectus femoris part of my quads.

Should I be concerned? Could this be a hip flexion problem? Or should I just continue to workout and hope that whatever muscle I may be hitting will stop causing me discomfort as it gets stronger? I don't think I've injured myself, but I could be wrong.

Try taking a week off squats, then cutting back to 1x per week on squats for a while and hopefully it will go away. Never push yourself through pain (except lactic acid pain) during lifting. It's just not worth an injury.