I have been having the same bug, and it does seem to occasionally fix itself but then come back.
Someone else on line that the bug happened when the landed at the Danger pad on Monarch and took out the nearby wildlife. I did the same and the bug seems to have happened sometime after that. However, once it happened, even very old saves (from well before I went to monarch) had the melee bug.
I think MeatpuppeT is right about the hitbox part of the puzzle, it seems when it happens that your hitbox for melee isn't where they are targeting.
