This issue is very frequent and has caused death on some occasions. It also happens in a few different ways.

-First way,
Even with the extra magazines in backpack, pants, or jacket... sometimes they will straight up not reload

-Second Way
If the magazine and bullet and chamber are completely emptied (even with fully loaded clips ready and available in inventory) pressing 'Y' will only single load bullets into the chamber instead of prioritizing the loaded clips

-Third Way
While using 'Y' to reload even with 3 or more clips readily available. The quick option go reload seems to only cycle between 2 clips

Note: I genuinely feel as though I may have missed a couple other ways this reloading mechanic screws up but cant actively or vividly remember. Some additional testimony to this glitch would be helpful