We see many flats with no obvious cause at work. I agree with the well over inflation of the tube out of the tire and placed in water to track the bubbles (or bubble after a few minutes when the puncture is really small).

Some flats are from poor air pressure maintenance, the tire pressure softens over the days/weeks and when ridded under inflated the tube rubs against the tire casing interior causing what look like directional sanding was done on it. The now abraded and thin spots can bleed air too slow to see bubbles or hear a hiss.

Another subtle flat cause we see more often than years ago is the wire puncture. The wire (from auto tire casings I think) get picked up in the tire and in time work their way through the casing to prick the tube. These holes are generally able to be seen, bubble track wise. But the wire can be hard to feel for, unless you reverse the direction you run your fingers along the inside of the tire. The wire is often at an angle that "lays flat" if brushed one way but will become "upright" if brushed the other way.

Valve core issues, dirt/bent core shaft or just not well tightened fully, happen but not as frequently as other causes IME. Still it is good form to check the valve core's tightness when installing a fresh tube. Andy.