There isn’t anything you can do but be mindful of overlap when riding? The old BS 6102 was very specific of toe overlap, but its lapsed and many manufacturers produce bikes, especially in smaller sizes, that have toe overlap
my Giant Defy Advanced is a medium, and I get toe overlap with my size 8 feet, bear in mind that is an endurance bike with a longer front centre and wheelbase. I had exactly the same situation with my 54cm Specialized Tarmac SL4
I only notice it when track standing at traffic lights, from to time if I rotate the bars my foot will touch the front tire.
It would never be an issue when riding at speed, as you don’t rotate the bars more than a few degrees as most of your turn is done by leaning