In terms of tracking all the chains, because of the dearth of testing in the beginning, I would suspect any shorter chains of transmission that didn't end in a super-spreader could easily be missed.

It is hard to get tested even now. It was essentially a catch-22. You could only become tested if you had contact with a proven case. But there were almost no proven cases, because you can only become a proven case if you had contact with a proven case.