After re-reading ... it has dawned on me that maybe you ran just a git pull. That will update current version to the highest in that series.
In order to 'upgrade' (which is different than 'update'), one has to issue the following commands *in the moodle code* directory:
git branch --track MOODLE_31_STABLE origin/MOODLE_31_STABLE
git checkout MOODLE_31_STABLE
While you at the command line, may as well finish the upgrade via command line:
git branch -a
should show the tracked branch is now the one you desire to upgrade to.
IF that's true:
php admin/cli/maintenance.php --enable (enables maintenance mode)
php admin/cli/upgrade.php --non-interactive
That will upgrade the DB.
Then take site out of maintenance mode:
php admin/cli/maintenance.php --disable
Make sure the files/folders belong to apache user group ... or however you set setup (ugh, jail user).
One could also purge the caches ... might need to do this ..
php admin/cli/purge_caches.php (takes no parameters/swtches)
Then hit the site with a browser, login and check things.
'spirit of sharing', Ken