Crates in the Half Life universe are not man-made objects. They are an independent life form -- most likely some kind of fungus -- with its own distinct lifecycle.
They may actually be aliens of some sort. I don't know enough of the backstory to be sure. But they clearly are not being manufactured for the purpose of storing things in. As far as I can tell, whenever you have some out-of-the-way, slightly damp place, crates will just naturally grow. Once in a while, someone will actually harvest one and use it for storing an object or two. But this is relatively rare: for the most part, they're just a mild nuisance that everyone has learned to live with.
I am not sure if this makes Gordon Freeman an exterminator, or if he is simply helping to spread the spores.