Some varieties of potatoes do grow long tops, especially if there is not enough light. They really need to be grown in full sun.

Onions, did you wait until the tops folded over naturally at the neck, or at least fold them over yourself, before lifting and did you also leave them on the ground to dry out a little before hanging up somewhere cool, dry and with good air circulation? Any onions with a thick neck should be used fairly rapidly as they won't keep and you need to check both onions and potatoes regularly over the winter and remove any that are starting to rot so they don't affect the rest.