When shoe manufacturers design shoes, they drill the cleat holes
roughly where the balls of the feet should be for that size of
foot. If you use a pair of shoes that are a size big, the cleat
holes will be further forward, which often makes it harder to
correctly position the cleat.
In the same way that people have different distribution of
length between the legs and the body, people have differently
proportioned feet (long toes and short metatarsals vs. short toes
and long metatarsals). It is especially important for people with
long toes and short metatarsals to not use shoes that are too big
as the balls of the feet are already further back.
Sometimes it's impossible to perfectly position the cleat fore
and aft due to abnormal distribution of foot length or strange
placement of the cleat holes. In this case, I would strongly
suggest changing to Speedplay which offer significantly more
fore/aft adjustment than any other manufacturer. If even more
adjustment is needed, I'd be looking to drill new cleat bolt holes
in the shoe.