Hi,

alert means that 2 or more different mods have modified versions of the same file.

You should decide which mod use and which not.

Expert modders can try (if possible) to merge both mods.

Exactly. When this error occurs it's because some stock files from the game can only have one existing version active at a time. Examples of this include things like the menu.xml, openGL shaders, etc. In order to create certain types of mods such files may need to be altered which would result in a conflict with another mod that had to change the same thing. This doesn't really apply to levels, weapons, and the like because, when done properly, they are more like "add-ons" and have a system in place to prevent such a thing.
Easiest example would be two people that create two separate mods. One simply changes the stars to Xs where as the other was a total conversion mod but also happened to change the stars to maybe something like circles. Because both of these mods are attempting to alter the same thing a conflict will result.

But as axios2006 points out, it may be possible to merge them but that depends on what is being changed and would require someone to manually look through it all to make such a determination.