Integrity check fails on user files (config & data)

Server
1

Just updated to the 9.1 from 8.1 and am runnning into the following issue

Steps to reproduce
1. backed up data & config folder
2. removed everything but those folders
3. updated OC

Expected behaviour
Everything works (better than before)

Actual behaviour
I know have a banner saying "There were problems with the code integrity check. More information…" and I get logged out all the time

Special configuration (external storage, external authentication, reverse proxy, server-side-encryption):
Nope

Integrity status for oC9+
See above

Technical information
=====================
The following list covers which files have failed the integrity check. Please read
the previous linked documentation to learn more about the errors and how to fix
them.
Results
=======
- core
    - EXTRA_FILE
        - owncloud/config/config.php
        - owncloud/config/config.sample.php
        - owncloud/config/.htaccess
        - owncloud/data/index.html
        - owncloud/data/.htaccess
Raw output
==========
Array
(
    [core] => Array
        (
            [EXTRA_FILE] => Array
                (
                    [owncloud/config/config.php] => Array
                        (
                            [expected] => 
                            [current] => 4058c229129ea5e9ead43fa41c8bc9f7070ea7ed9baed84f9bff9716a99f3342ccf36e9f7ee8cc67c66cf98027c0e248c6787ade15679a212d285cdc723e80e5
                        )
                    [owncloud/config/config.sample.php] => Array
                    (
                        [expected] => 
                        [current] => 0f59bdecb5d4729b9a6f5faaee3fc70cb93e0ddb1e600dadb30e865ade9d051c90b7de732a10d0416a68f7af389742d67b4e9b038530404a979023444ba47ee3
                    )

                [owncloud/config/.htaccess] => Array
                    (
                        [expected] => 
                        [current] => 7d905d5e14661b2fb2baae54c8925185c61c002d33d396112ac94aaa20865359861e4169d1a07f2b5375f99ab08f3921225c30861b74629c0caa020dffb85322
                    )

                [owncloud/data/index.html] => Array
                    (
                        [expected] => 
                        [current] => cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e
                    )

                [owncloud/data/.htaccess] => Array
                    (
                        [expected] => 
                        [current] => 9f6523b5fe5f7d23c30ef93aeb9a1cd21a2e50cc5723d968250ab664f2334d7bfdd4cc212c4290d1963d1cc849c1fa159e59495616e1f03daae8d2073a112158
                    )

            )

    )
)
2

Mhhh, any chances that you have doubled folders like:

/var/www/owncloud/data

and

/var/www/owncloud/owncloud/data

? The extra_file in this case means that you have files there which oC doesn't expect to be there.

3

@RealRancor - fixed it! I initially installed it in an "owncloud" sub(-sub-)folder and forgot the one clean up of these files that I left there when moving the rest one level up.

I ran a re-scan after deleting those files and the error msg disappeared.

Thanks for the quick and helpful reply!