There are many reasons, some due to using tools, which is why, once the repair is set, I put the tube back in the tyre, only with my hands. Then I put a bit of air only, to reduce the liklihood of pinching the tube between rim and tyre, then again, only using my hands, I slip the tyre wall back into place.
On some fat or specialised tyres, that may not be as easy as I make out here though!
Also, years ago I had a similar problem, and I found a bit of a thorn, had gone into the tread, was totally invisible, but was holing the tube, but only once air pressure was built up, but as it only came a tiny amount, less than 1 mm, into the tyre, I had to ride to cause the next hole.
Two ways to handle it:-
1) run your hand around the inside of the tyre and feel for the thorn.
Always marking the tyre with the position of the valve, and knowing the direction of the tyre, makes that easier as you know roughly where to look!
2) Take an old tyre, cut off the walls so that you just have the worn tread. Place that between the current tyre tread and the tube, it gives quite a good protection and is really cheap! Give it about a 2 centimeter overlap when installing.
Best of luck
Andy