It's probably not an issue of the hip flexor(s) being too short, so stretching probably isn't the best fix for your issue.
It's hard to give concrete advice based on your description, but I'm going to take a stab at it and say that the pain is worse at the bottom of your squat. If you could post a video of your squat form that would be super-awesome, but just from personal experience:
Usually, when I have a client who complains of tight hips when they squat (or when mine start getting creaky) the issue is almost never at the hip. This is especially true if they feel that pain and tightness in their hip flexors at the bottom of their range of motion. At that point in the squat, the hip flexors are in a shortened position; they're not being stretched, so it's not an issue of length, and stretching them isn't addressing the problem.
What might be happening -and this is just a guess- is that that sucker is holding on for dear life because it's trying to provide stability to your core. There are lots of "hip flexors", but in a general fitness sense, when we refer to them, we're talking about one in particular called the Psoas. It inserts at the inside/front of your hip (the area where you're jacked up) and attaches to your lower back. Believe it or not, it's actually a part of your core, in the sense that it plays a role in spine stabilization.
So if the other muscles around your lower back aren't doing their job to stabilize your back, the psoas might try to pick up the slack.
So, that's one theory.
The other is that, whether you can tell or not, your knees are caving in a bit, and it's irritating that muscle and/or your hip capsule.
In either case, try these cues:
Brace your core. If you don't know what I mean, imagine someone is about to roundhouse-kick you in the gut, and you need to break their foot; every muscle around your midsection, and I'm talking front, sides, back, and every angle in between, should get rock solid.
Alternatively, and also more scatologically, imagine you're taking the biggest dump of your life. Should result in the same braced core, but hopefully not a ruined pair of Andrew Christian's.
This is what you need to do at the top of each rep. Take a big gulp of air, put it in your gut, brace hard against it, hold it as you descend, keep holding it until you're halfway up, and then finally let it out. If a weak core was the reason your hip flexor was lighting up, this should fix it (it would also explain why the problem only occurred when you increased the weight).
The second cue is this: "spread the floor" during your reps. That basically means pushing your feet out against the outside of your shoes as you approach and come out of the bottom of the squat. When you do this (do it now! Do it, no weight required, go!!) you should feel the outside of your hips turn on. You know, your butt. Your butt helps keep your knees from caving in, and also it can look nice, so make sure it's working in your squat.
My third suggestion...wait, did I say I only had two? Sue me: Foam roll like you're getting paid to do it. Specifically, your IT band, hip flexor, quads, adductors, and glutes. If you have no idea what I'm talking about...uh, never mind. Whole 'nother wormhole.
Try these during your next squat session, and see if they help at all. If it/they work, then you've identified the problem, and now you know how to fix it.
If you have any questions, I obviously love geeking out about squat mechanics.