Why are two different "Well" cards included in the new version of Agricola?
The Well that shows three Stone and one Clay is a misprint, which was packaged up with the rest of the cards. The other well was included separately from the rest of the cards as a replacement to fix it. So you should only use the one that is the same as the original version, that costs three Stone and one Wood.

Sources for this information:

https://boardgamegeek.com/thread/1695453/2016-version-extra-well-major-improvement-card-box

and

https://boardgamegeek.com/thread/1587110/extra-well-card