And in don't understand why or what it's doing. Is this something to worry about? How did it happen?

Wow...

They're just adding the default .ini with tweaks to use their mod correctly. Nothing to be concerned about, just overwrite.

EDIT: Give me more info. You're not being clear enough.

No, i mean my mod made it, nothing i've downloaded.

I'm not sure what more to add, when backing up manually i noticed that spire.esp also suddenly had a spire.ini. It is incredibly long with a extreme amount of options, i've not written it manually, but i guess i may have fatfingered a button somewhere.

Don't worry, everything is fine. Mods make files of their own to help them run, I've seen some mods that make multiple .ini's.

Ah okay, i'll let it do it's own thing then. Thanks!

You're very welcome .

Also, try exploring your .ini files to see if you see any settings you'd like to tweak.

Just delete it if it's not supposed to be there. The console command, RefreshINI, makes for such INIs that will have every single INI setting. You don't want or need such INIs hanging around as they will override Skyrim.INI, SkyrimPrefs.INI, and other mod INIs (their precedence determined alphabetically and not by load order).