Shortly after changing a flat in a dirt road near home, I got another one. This last tube got a very small puncture. Inside the tire I also found some small pebble (like 1mm or less in length), but no thorn or wire.
I wonder if this small gravel trapped inside the tire can puncture the tube?
If the pebble was sharp, it definitely could be the reason. Each time before you change the tube, check the tire from the inside for any thorns that stuck or (something that happens quite often) glass particles that left inside. Using sealant tubes could be another great idea if your main riding is off road (I think that without them I would be changing tubes two times a ride).
More likely you punctured the tube while installing it. You have to be careful to not pinch the new tube between the rim and the tire. Also take care not to puncture the new tube with your tire levers.
When changing a tire I'll inflate it the tube about 50% and then peel the tire around to make sure the tube is not pinched. Then I deflate and the reinflate to recommended pressure. I use plenty of lube on the bead too. That can be water or better but grosser, spit.
The amount of friction between the casing and a tube is impressive, especially over time (there's a photo out there that I tried to find to illustrate it but failed- if anyone can find it feel free to edit), but if you don't see an obvious spot where it looks like the tube "wore through" then you probably had a puncture where the offending object simply fell out.
