Generally it's best if a dual-licensed project is explicitly described as such in all the places where it is distributed, but there's no legal requirement for that to happen. Legally, the license which you acquired it is the license that you have to abide by. So if you download it from their website then use it under the MIT license, if you download it from GitHub, use it under the Apache license.
I guess the one case where it would matter is if you want to redistribute it yourself under both licenses. Unless one of the sites explicitly offers the project under both licenses I don't think it would be legal for you to redistribute it under both.