I think the biggest issue is that it makes it hard for programming environments to pick the right syntax coloring. There may also be problems selecting the MIM

I think the biggest issue is that it makes it hard for programming environments to pick the right syntax coloring. There may also be problems selecting the MIME type when serving the file. So if you have to use a conflicting file extension, you probably want to use one that isn't already associated with a major programming language or web file type.