I have the same problem, it seems like various files got locked up.
Here is the exception I got when scanning NC for externally modified files:
Starting scan for user 2 out of 5 (Daniel)
Exception during scan: File entry could not be inserted with insertIfNotExist() but could also not be selected with getId() in order to perform an update. Please try again.
#0 /var/www/nextcloud/lib/private/Files/Cache/Cache.php(230): OC\Files\Cache\Cache->insert('files/07_AutoUp...', Array)
#1 /var/www/nextcloud/lib/private/Files/Cache/Scanner.php(292): OC\Files\Cache\Cache->put('files/07_AutoUp...', Array)
#2 /var/www/nextcloud/lib/private/Files/Cache/Scanner.php(221): OC\Files\Cache\Scanner->addToCache('files/07_AutoUp...', Array, -1)
#3 /var/www/nextcloud/lib/private/Files/Cache/Scanner.php(435): OC\Files\Cache\Scanner->scanFile('files/07_AutoUp...', 3, '2402', false, true)
#4 /var/www/nextcloud/lib/private/Files/Cache/Scanner.php(403): OC\Files\Cache\Scanner->handleChildren('files/07_AutoUp...', true, 3, '2402', true, 1493425852)
#5 /var/www/nextcloud/lib/private/Files/Cache/Scanner.php(406): OC\Files\Cache\Scanner->scanChildren('files/07_AutoUp...', true, 3, '2402', true)
#6 /var/www/nextcloud/lib/private/Files/Cache/Scanner.php(406): OC\Files\Cache\Scanner->scanChildren('files/07_AutoUp...', true, 3, '2399', true)
#7 /var/www/nextcloud/lib/private/Files/Cache/Scanner.php(406): OC\Files\Cache\Scanner->scanChildren('files', true, 3, '304', true)
#8 /var/www/nextcloud/lib/private/Files/Cache/Scanner.php(337): OC\Files\Cache\Scanner->scanChildren('', true, 3, '302', true)
#9 /var/www/nextcloud/lib/private/Files/Utils/Scanner.php(244): OC\Files\Cache\Scanner->scan('', true, 3)
#10 /var/www/nextcloud/apps/files/lib/Command/Scan.php(161): OC\Files\Utils\Scanner->scan('/Daniel')
#11 /var/www/nextcloud/apps/files/lib/Command/Scan.php(234): OCA\Files\Command\Scan->scanFiles('Daniel', '/Daniel', false, Object(Symfony\Component\Console\Output\ConsoleOutput), false)
#12 /var/www/nextcloud/3rdparty/symfony/console/Command/Command.php(264): OCA\Files\Command\Scan->execute(Object(Symfony\Component\Console\Input\ArgvInput), Object(Symfony\Component\Console\Output\ConsoleOutput))
#13 /var/www/nextcloud/core/Command/Base.php(161): Symfony\Component\Console\Command\Command->run(Object(Symfony\Component\Console\Input\ArgvInput), Object(Symfony\Component\Console\Output\ConsoleOutput))
#14 /var/www/nextcloud/3rdparty/symfony/console/Application.php(874): OC\Core\Command\Base->run(Object(Symfony\Component\Console\Input\ArgvInput), Object(Symfony\Component\Console\Output\ConsoleOutput))
#15 /var/www/nextcloud/3rdparty/symfony/console/Application.php(228): Symfony\Component\Console\Application->doRunCommand(Object(OCA\Files\Command\Scan), Object(Symfony\Component\Console\Input\ArgvInput), Object(Symfony\Component\Console\Output\ConsoleOutput))
#16 /var/www/nextcloud/3rdparty/symfony/console/Application.php(130): Symfony\Component\Console\Application->doRun(Object(Symfony\Component\Console\Input\ArgvInput), Object(Symfony\Component\Console\Output\ConsoleOutput))
#17 /var/www/nextcloud/lib/private/Console/Application.php(173): Symfony\Component\Console\Application->run(Object(Symfony\Component\Console\Input\ArgvInput), Object(Symfony\Component\Console\Output\ConsoleOutput))
#18 /var/www/nextcloud/console.php(90): OC\Console\Application->run()
#19 /var/www/nextcloud/occ(11): require_once('/var/www/nextcl...')
#20 {main}
The fun thing is that no problems occured when i uploaded it from my PC but when i try to sync it with my laptop I get various “file is empty, although server reported x size…” errors, but just for (I think tey are the same) those few files.