It's not gremlins. Each hole has a cause, and it's quite possible there are multiple causes.
If it happens again, then when removing the tube make note of exactly where the tube is in relation to the tire and the rim. Use a sharpie or tape or something to record exactly how they were aligned. Then find the hole as before. Inspect the tire and/or rim where the hole aligned. Use your eyes, a magnifier, your fingertips to feel, a ball of cotton drug along the surface looking for something sharp. Or a hole in the tire where something came and left. Find it, fix it, repeat.