The UPS program Tsukuyomi is unable to patch the ISO. Use NUPS if on windows. Use Multipatch on Mac.
Apply the patch file to a clean Pokemon XD: Gale of darkness ROM using any UPS patcher. This patch was made for the NTSC (US) version so it will not work on other versions. The ISO is quite large so it may take a few minutes.
Always patch onto a clean ISO, even if you are applying an update.
The file size for the ISO should be 1.46 GB (1.35 GiB). If it's an nkit (1.1. GB) ISO then you'll need to convert to a regular ISO using this tool. Drag and drop the ISO onto the program called "ConvertToISO". Once it has finished the full ROM with the correct file size will be in the folder called "Processed". Apply the patch to that ROM.
If the file size is below 1GB it's probably in a .zip, .7z, .rar or other archive and needs to be unzipped.