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It's with physical attacks, that's why it's so confusing.

My theory is that you had an augment equipped that made your physical attack an elemental attack.  Then I changed the augments in the game to no longer do that - but because if the way augments work "under the hood", they change the players stats and then remove them when the augment is removed (So the new augments would not remove the effect even when removed from the weapons/armor).  That would mean that as long as your game was started on a more recent version (after the augment changes), this should no longer occur.  I will keep an eye out for it though - as my theories can sometimes be incorrect :-)