I don't know if that might have caused any problems, the standard is short extensions so I am just following suit.
Perhaps I'm nitpicking, but to be completely correct it should be pointed out that the short extensions were the standard years ago. They are no longer considered "standard". We have a lot of short extensions because they are a legacy and have been short for so many years, that it would be counter-productive to change them just now. It would confuse people.
However, for new programs, like MyDefrag, it's better and recommended to use longer extensions, to avoid collision with other programs.
Take a look at Microsoft, for example. They have also started to use longer extensions (.manifest
files are a good example)
Also, using a unique extension gives you, as a bonus, the possibility of having an exclusive icon to recognize your files. Right now you are clashing with people who had personalized MySQL files with their own icon.
Given that MyDefrag is still a beta, I think it wouldn't be too disruptive to change the extension. It would cause very few inconveniences in the short term, and be better for the long term.