It means the modder muddled up
What I sometimes find myself doing is having to edit the .MOD file accordingly so EasyMOD will read it correctly. I haven't come accross any problems with EM, but I do find it is only as good as the modder himself. If there's errors, EM is useless until resolved.
Try opening the .MOD file and (backup first) locate the section of code you are struggling with. Perform the task manually and then delete the code from the file. Sometimes you might need to manually copy individual files to their correct lcoation.
I tell you another thing to watch out for. Sometimes the mod will request a "FIND" which is successful, and will then request another "FIND" for a section of text it has already gone past. As with notepad, it just doesn't like it, and will reach the end of the document. Therefore you might need to play around with some.
Best solution is to go for the EM Comliant Mods, which are obvbious by the Logo next to the entry in ACP.
Also take into cosideration the over the course of new phpBB versions, the code will change. For this reason, a Mod for 2.0.x might not work for 2.0.13 unless you specifically ammend the outstanding details.