I made this exact mistake on a 320-acre purchase back in the early 1990s. Paid fair market value, shook hands, felt good about it. Found out six months later that mineral rights had been severed three owners back and I had no claim to anything beneath my topsoil. Nobody volunteered that information, and I didn't know to ask.
In western Kansas, severed mineral estates are extremely common. I'd argue they're the rule, not the exception, on any ground that sat inside historical oil and gas leasing country. But I've seen buyers from wetter states come in completely blindsided because where they're from, surface and mineral rights almost always transfer together.
A title search alone won't protect you. You need someone who actually reads the chain back far enough to spot a severance, not just confirm current ownership. That's a different skill and sometimes a different cost.
If you purchased in a region with active oil, gas, or mineral extraction history, did your closing attorney treat the mineral title as a separate research task, or did it get lumped in and glossed over?