Question

Why did one liter of have a greater mass than the other liter prepared by a different method

Answer 1

Maybe the water wasnt stable enough and probably couldnt read the water level correctly

Answer 2

Nobody can answer your question, because we have no idea
what belongs after the word "... of ...", so we don't know what
substance(s) you're talking about. 

All we can say for sure is that the first method produces the substance
with greater density, because it has more mass in the same volume.