Yes, happens to me too, and I’m a petite size 11. The Ultimate Clutch Pedal didn’t help with this clearance issue, but it sure did get rid of the annoying inches of dead space travel and lack of feel in the stock clutch pedal.
I’ve also noticed that the clutch and brake pedals seem a bit too close to each other, so that I occasionally catch the edge of the brake when depressing the clutch pedal. Makes for an unpleasant surprise when you’re accelerating up an on-ramp, shifting from 2nd to 3rd, and you accidentally tap the brake.
Sneakers/trainers or other shoes with a wider toe box make this a real annoyance.