Possible root cases could be that files came as a result of a cross project merge Or if there has been any refactoring for this file, or the folder.
The way to get past this problem is:
1. Check out version 0 from the new package to a temporary folder (like C:\Temp1)
2. Delete both version 0 and version x.1.1 from that package with the "Delete Version" process.
3. Check out version 1 of this file from package ... for update to a second temporary folder (like C:\Temp2)
4. Copy C:\Temp1\your_file to C:\Temp2\your_file, replacing the file that was there
5. Check in the file from the C:\Temp2 folder.