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The Species problem is a dilemma facing Biologists (Taxanomists and Phylogeneticists to be more specific). This dilemma is what it takes for two species of the same Genus from one another.

Now one would say "obviously its that's they can't produce fertile offspring"

But that's the dilemma. That requirement is steadily becoming outdated. As new evidence shows that Neanderthals and Homo Sapiens regularly interbred with each other. And new breeds of canine dubbed Coywolves (coyote and wolf hybrids) have been shown popping up in the wild, and they are fertile.

So how exactly could we solve this problem?

Thanks for the topic OP, I never heard of it.
I really only have high school biology to go by, so I don't really know what I can propose, and even if I do it will probably be full of holes. The best guess I can make is, well, you know how there are subphylums, (or maybe I'm remembering things wrong)? Well, are there subgenuses? If not, maybe species that can have fertile offspring together belong under the same subgenus.

That's really all I got though, without doing more research.

I feel like what we should do is take DNA samples from certain species of animals and make a limit to how different each sample can be from one another to be classified as a different species.

"What is a species?" can only be answered with "What is your major?" because nobody is going to give you the same answer, which I guess sums up the problem of The Species Problem.

To an ecologist like myself, a "species" is a lineage that occupies a (nearly) unique adaptive zone compared to any other lineage in its range, which is also evolutionarily distinct from lineages outside of its range.

A biologist would say "groups of actually or potentially interbreeding natural populations which are
reproductively isolated from other such groups."

A geneticist would say it's a "group of organisms so constituted that a hereditary character of any of these organisms may be transmitted to a descendant of any other."

There are tons of definitions in use today, and there will probably never be one we can agree on.