As a practical matter, coffee and cola are so available that it is hard to argue that runners drinking cola have some illicit advantage. Caffeine is not a banned substance under USOC rules unless it is taken in very large doses, equivalent to 8 cups of coffee. It is a di-peptide of apartic acid and phenylalanine. Both of those are very common in foods with any significant protein content. Phenylalanine is an essential amino acid, so the body can handle it quite easily.
Aspartic acid is a very common amino acid.
If that were true, the compound would cause widespread blindness and nerve damage, and would never have been approved for food use. Small amounts of methanol are produced in the metabolism of aspartame, but the body can detoxify those amounts. According to the literature, more methanol is produced by the metabolism of a tomato than a can of soda sweetened with aspartame. I never met a carbohydrate I didn't like, so I rarely have anything with aspartame in it, but when I do, no sleep is lost over the matter. As far as being a source of calories in a soda, the amounts are so small that it is essentially useless.