Got two flats in 24 hours a few days back. I just switched out to the spare tube on the trail in 10 minutes or so and did a quick check. I couldn't find any obvious reason. Put the new tube in, rode home and 3 hours later it was flat again. I had to pump the tubes up to operating pressure and immerse them in water to find the tiny pinholes that caused it.

Then I checked inside the tire and found the worlds smallest metal shard. How it got in there I have no idea but it was that few mm of metal that caused it. Its amazing what can cause a flat tire.