A very clever alien..

[downbeatplumb]

The answer is simple, check their breath and look for signs of the pieces of dinner in their mouths. Farts also smells like food naturally. There are many different things the alien could try, such as check of signs. and clues. The alien could ask his wife who made him the dinner about the kids, she might have gave the dinner to one of the children. He could also see or remember what kind of foods the kids like to eat, and if they have any allergies. 
By the way the theory of everything can keep going on. I and the bible believe in progressive intelligence, i do not believe in evolution, things tend to mix or develop someway, this works with some animals, etc but it does not apply to humans evolving from apes. Animals can evolve through circumstances, did you know that the shape of a child's head can naturally be different from another due to how they come out of the mothers vagina. One person sees a big head in his back garden, and thinks it was an ancestor, giants existed long ago according to both science and scripture.

"Science" does not agree that there was a race of giants.

Find Out How the Giant Skeleton Hoax Started (nationalgeographic.com)

Interestingly the phrase "Theres a sucker born every minute" was first coined about people paying to see a fake giant.

Cardiff Giant - Wikipedia

So no there were never giants. For one thing you cant just scale people up and have a working person. There is a reason that elephants have a very different structure to mice.