Because they don't have the same standard. Coinmarketcap is the oldest cryptocurrency encyclopedia. And I think it's more credible than coingecko. Coinmarketcap has a higher standard like the altcoins must be on at least 4-5 Exchanges in able to list them on the platform. They only list good altcoins and they make sure that the  altcoin they list is trustable. Coingecko can be paid by the I think.