There's an argument for atheism that goes something like this: some animals have nonfunctional parts, proteins, DNA, &c. That's what we'd expect if naturalistic evolution is true. Although that doesn't falsify God's existence, it makes theism less probable than atheism.
There are different ways of responding to this argument. I'd like to focus on just one. Recently, as I was strolling through a public park, I noticed that someone left a spade behind. I assume it belonged to the groundskeeper.
I don't normally pay much attention to garden tools, but one thing happened to catch my eye: the tip of the handle had a square hole or aperture. Now that's a nonfunctional feature. That doesn't made the spade a more efficient digging tool. It doesn't improve the functionality of the spade.
If we were examining the spade from the standpoint of a secular evolutionary biologist, we'd conclude that this nonfunctional feature was the byproduct of an undirected process.
Now, since I don't design spades, I can't say with authority why the tip of the handle had a square hole. However, having been inside my fair share of hardware stores, I will make a wild guess: that's a built-in feature so that you can hang the spade on a wall or rack. It's a convenience.
Although that feature doesn't contribute anything to the functionality of a spade as such, it is useful in relation to something else: it makes the product easier to display or to store. Of course, if you were unaware of that larger context, you might draw the false inference that this was a pointless feature.
In regard to biology, it's possible that some features which seem to be nonfunctional in relation to the organism itself may be functional in relation of the environment, of which the organism is a part. There's a sense in which the ecosystem is one big symbiotic network.