If you don't follow this guide you may often run into issues...either the mod won't show up in game or it will give you last exception files.
Make sure the modder/creator has specified that the mod has been updated.
Before you put the new version in your folder completely delete the old version and every part of that version. You should not get this pop up if you have fully deleted the old version:
There should be no "existing" files of the old version to replace.
If you do not delete the old version before adding in a new version you can get errors, the mod or some of it won't show up in game, or it may even cause major bugs. When you use the replace option you are mixing old and new files.
After you have made sure the old version is deleted put the new version in.