It is possible that a Li-ion cell takes in more charge during a full charge than it gives during a full discharge.
The ratio of the two values is called the "Coulombic Efficiency" (Or Faraday efficiency).
CE = (charge taken during a full charge) / (charge given in a full discharge)
Normally, a Li-ion cell has a CE of 99.9 % at room temperature. That means, for every 1000 electrons you put into it, you get back 999 electrons. (The missing electron is lost due to a Li+ ion being lodged in an electrode as Li metal. It's non-reversible.)
The CE gets worse at low temperatures, on the order of 95 % at 0 degrees C.
If your cells show a CE noticeably less than 99 % at room temperature, either the test is flawed, or the cells are really in bad shape.