I had a problem with files with an apostrophe character like in File:Kiessling's_Kleiner_Verkehrsplan_1904.jpg. For such files in Wikimap Warper the rectify tab doesn't show anything. I had to change the file name in Wikimap Warper temporary and after the rectifying change it back to the old file name, cause otherwise the link from Commons won't work anymore.
Example:
http://warper.wmflabs.org/maps/209
http://warper.wmflabs.org/maps/209/warp returns "500 Internal Server Error"