Getting the same two hash values for carved files I found
It is quite practical to deliberately generate two different files with the same MD5 hash; if you were handed these files by someone else, it is possible that they did this.

However, MD5 will collide only if someone deliberately crafts the files to do so; if you modified the files somehow, then this is unlikely to happen.  Instead, it would be a strong indication that the two files are bitwise identical.