So I changed my program today – and one element I changed was to do squats rather than lunges. I had worked up to 40 lbs on each side of the bar and figured it was pretty much the same muscles so started at 35 lbs/side for the squat. Did the first two sets of 10 just fine. Started going for the third and my whole fucking thigh went crazy, causing me to stop immediately. I finished my workout, took a naproxen and knock wood didn’t cramp up. But Holy Jesus did my thighs hurt – and I expect getting up tomorrow’s going to be fun. But I just consulted my newly bought “Strength Training Anatomy” and see that the muscles are in fact pretty much the same. What gives? Are squats harder than lunges?
No, you’re just using them differently. For some reason this causes soreness and possible cramping during the exercise. I get the same sort of phenomenon when I do lunges instead of squats.
Others on the forum might have a real answer for you though.
Since lunges are more of a single-leg exercise I would have thought you could squat more than you can lunge with, but I’ve never done them with any weight so I’m just guessing.
I always find that lots of fluid is important during any sort of extended exercise. Remember that you’re moving not just the bar but your bodyweight, so 30 squats is no small matter.
See how you feel in the morning, and then sign up for the mandatory 5/3/1 training program 
Ah, The Law of Specificity.
It’s nothing to do with one exercise being harder than the other and it doesn’t matter if the muscles used are the same or not, if the movement pattern is new to you, and it only has to be slightly different, muscle fibre recruitment will change and soreness will result as fibres are recruited at different times and levels. You’ll adapt really quickly though.
The silly thing is, a few weeks of squatting and going back to lunges will make you sore.