I think there were several theories. Basically to get this 'Positive' and Mirrored artifact of the reverse side of the coin, the die has to have a negative impression on it. So there has to be contact and some form of interaction between the 2 dies. The 2 theories that I liked and thus remembered are as follows:
1) There is a dies clash, and one of the dies is heavily damaged, there is an are with 'Positive' impression of the opposite die on the damaged die. The damaged die is filed down to remove this damage. The metal in the filed down are is softened, and over time indentations develop from heavy use, that end up producing 'Positive' impressions on coins. I'm not a metallurgist so can't tell if this is likely.
2) The other theory had to do with rust. Let's say that dies are in place, but the press is not used. So the two dies are just sitting there in contact with each other. Over time rust sets in, rust in the contact areas is more aggressive (not sure why). After some time, the press is prepared to be in use, the workers scrub the rust off, but now there are indentations in the places of die contact that cause Positive impressions on coins.