This is probably because pre-punching makes small ridges on the bottom of the card, and an identical pattern of small troughs on the top. The ridges tend to get caught in the troughs. Also, feed mechanisms have to be engineered with consideration of the air cushion between the cards, as one moves relative to the other. For whatever reason, misfeeds happen. Hanging chad can flip open and closed.
Detached chad can become stuck in the feed path, increasing double feeds and misfeeds.
Detached chad can jam two cards together, increasing misfeeds. In some machines, detached chad can jam over the light or sensor, causing holes to not be read until the chad blows out of the way. Detached chad can migrate from one card to the next. People can not count cards as quickly as a card reader, but a card reader is much more limited than a person in how it can handle and read a card. Any damage a card has sustained can, as we've seen, confuse a card reader or cause it to malfunction.