I also find that squatting takes it’s toll on my hip flexors… but static streching beforehand really helps. Try getting down on the floor and into a “butterfly” (or whatever you want to call it)with the soles of the feet together. Then place a 25lb. plate on each knee. Focus on keeping your feet close to your body and your torso upright, and let the plates pull your knees to the floor. It’s best to do some bodyweight squats or something similar to get the hip flexors a bit warm first, maybe some lunges. I got this trick here on T-Nation, though I can’t remember from who (maybe Don Alessi?). This isn’t really a full warmup, but a nice trick.
In addition, I usually do some dumbell swings and GHRs to loosen up my hammys, and I go up slowly with the loading. If you squat on a box, you can start with the box 2-4" higher than you use for your working sets, and lower it as your hips get loose. Hope this helps…