A user's MySite is over the default quota of 100MB.
PS C:\> $site.Usage.Storage 106731646
So the user currently has round about 106MB in his personal site. The problem is: He doesn't.
SELECT SUM(Size) FROM [SP_Content_MySites].[dbo].[AllDocs] WHERE DirName LIKE '%personal/username%' AND SIZE IS NOT NULL AND SIZE != 0 --> 3993036
So he actually has 3,9MB in his personal site.
I checked his recycle bin (that's where the 3,9MB comes from) as well as the second stage recycle bin (empty). I don't know where the 100MB comes from and I don't know how to "update" the quota - by that I don't mean to increase it. Is there some cleanup timer job I need to run? Any more Powershell voodoo I can try?