There are a million different things that can go wrong with ROM's and patching.
Are you sure the ROM file you have is a clean dump to begin with?
Are you sure it is the correct revision of the game targeted by the patch (some games have multiple releases/revisions)?
Is the patch you are using even meant to be used on a clean dump?
Have you tried running the ROM file without the patch?
Can the ROM run in an emulator?
EDIT - I see that Tomodachi Collection was never actually released in English, suggesting you have already applied a translation patch. Patches on top of patches are no bueno.