Can small pebble inside tire puncture the tube? 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).