If you try to relog, to correct the issue, the gun then continues to have a magazine in it, but refuses to let you remove the magazine. After all the bullets are emptied from the gun, if it is an automatic, you can click on full auto, giving the empty chamber click, but as if you are firing, full auto.
After more testing, it would appear the issue is only reproduced, when using the new R to reload mechanic. Though it still, does seem random when it occurs.