TwentyEleven 1.5 (official)
TwentyTen 1.5 (official)
---> Though I use a custom template and TwentyEleven/TwentyTen is deactivated
Yep, same thing happened to me. I saw the WP alerts that TwentyTen and TwentyEleven needed updating.
I don't use those themes, but thought I'd update 'everything' (a Wordfence update was due roughly around the same time).
Got the alert a couple hours ago (even though I updated everything about 12 hours ago).
* WordPress core file modified: wp-content/themes/twentyeleven/functions.php
* WordPress core file modified: wp-content/themes/twentyten/functions.php
Yep, official update (for TwentyEleven and TwentyTen).
Very strange. Am considering just deleting those two themes (since I don't use them) -- but it's always good to have something in there other than a custom theme (for testing purposes I guess). Not sure if that's a silly habit of mine, or good-practice in WP. (I know in Joomla we'd rarely ever delete the default themes Beez and so on -- cause they get used for late-night live testing when the 'main' custom theme has issues).