Thinking about this a bit more, I am going to agree with those who are suggesting a saddle / bike set up issue.
After all, people ride all sorts of bikes in all sorts of shoes - I've ridden my road bike, which has SPD-SL pedals (basically triangular or D-shaped pieces of metal that are intended to have specialised shoes clipped to them) while wearing trainers (and I think even flat-soled office shoes) and I'd ride my folding bike (with flat pedals) wearing pretty much any shoe I own (including the ones with heels) - the exception being my fell-running shoes which have big chunky studs on the bottom which would catch on the pedals.
After all, people ride all sorts of bikes in all sorts of shoes - I've ridden my road bike, which has SPD-SL pedals (basically triangular or D-shaped pieces of metal that are intended to have specialised shoes clipped to them) while wearing trainers (and I think even flat-soled office shoes) and I'd ride my folding bike (with flat pedals) wearing pretty much any shoe I own (including the ones with heels) - the exception being my fell-running shoes which have big chunky studs on the bottom which would catch on the pedals.