Suppose you have weapon A and B, A being equipped. Now you attempt to pick up weapon B. What happens is:

• Weapons are switched, which is the best option since there is no dual wielding.
• However, the drop/pickup code acts as if you now have two B weapons, turning the weapon on the floor into weapon A.

Basically, you have turned a B weapon into an A weapon.

EDIT: Reported for 0.9.1