I've always drained and ran dry...yes you can get stuff in your fuel jug....I can't swear to ya where the stuff comes from...off the pick up line? from the cap? or from the tank...moisture in the fuel can come from contensation going from hot humid summer weather with the cap open ( lines in the cap for refueling is still open to atmosphere) to cool garage floor or worse air conditioned car...
When the fuel jug gets low I'll look in the jug and see how much contamination, if any, there is. If there is some I won't use the last bit of fuel...And never ever pour the remains from one jug of fuel to a new jug.