Schemata error during upgrade

During phabricator upgrade (from commit 4c242256e4 to f0f352ffd0 on stable branch) I got a "SCHEMATA ERRORS " message, and instruction that I should report this.

Here goes the full log:

[phabricator@capricornus phabricator]$ ./bin/storage upgrade
Before running storage upgrades, you should take down the Phabricator web
interface and stop any running Phabricator daemons (you can disable this
warning with --force).

    Are you ready to continue? [y/N] y

Applying patch "phabricator:db.paste" to host "localhost"...
Applying patch "phabricator:20190718.paste.01.edge.sql" to host "localhost"...
Applying patch "phabricator:20190718.paste.02.edgedata.sql" to host "localhost"...
Applying patch "phabricator:20190718.paste.03.paste.sql" to host "localhost"...
Applying patch "phabricator:20190718.paste.04.xaction.sql" to host "localhost"...
Applying patch "phabricator:20190718.paste.05.comment.sql" to host "localhost"...
Applying patch "phabricator:20190802.email.01.storage.sql" to host "localhost"...
Applying patch "phabricator:20190802.email.02.xaction.sql" to host "localhost"...
Applying patch "phabricator:20190815.account.01.carts.php" to host "localhost"...
Applying patch "phabricator:20190815.account.02.subscriptions.php" to host "localhost"...
Applying patch "phabricator:20190816.payment.01.xaction.sql" to host "localhost"...
Applying patch "phabricator:20190816.subscription.01.xaction.sql" to host "localhost"...
Applying patch "phabricator:20190822.merchant.01.view.sql" to host "localhost"...
Applying patch "phabricator:20190909.herald.01.rebuild.php" to host "localhost"...
Storage is up to date. Use "storage status" for details.
Synchronizing static tables...
Verifying database schemata on "localhost"...


Database                 Table                 Name         Issues
phabricator_differential differential_revision phid         Surplus Key
phabricator_differential differential_revision key_modified Missing Key
phabricator_differential differential_revision key_phid     Missing Key
phabricator_phortune     phortune_accountemail key_account  Missing Key
phabricator_phortune     phortune_accountemail key_address  Missing Key
phabricator_phortune     phortune_accountemail key_phid     Missing Key

Found 6 adjustment(s) to apply, detailed above.

You can review adjustments in more detail from the web interface, in Config > Database Status. To better understand the adjustment workflow, see "Managing Storage Adjustments" in the documentation.

MySQL needs to copy table data to make some adjustments, so these migrations may take some time.


    Apply these schema adjustments? [y/N] y

Applying schema adjustments...
Done.                                                                         
Completed applying all schema adjustments.

Target                Error
phabricator_dashboard Missing
phabricator_daemon    Missing

 SCHEMATA ERRORS 

The schemata have errors (detailed above) which the adjustment workflow can
not fix.

If you are not developing Phabricator itself, report this issue to the
upstream.

If you are developing Phabricator, these errors usually indicate that your
schema specifications do not agree with the schemata your code actually
builds.
 ANALYZE  Analyzing tables...                                                 
Done.                                                                         
 ANALYZED  Analyzed 512 table(s).

Subsequent ./bin/storage upgrade prints that “Storage is up to date” and the same error; full log below:

Before running storage upgrades, you should take down the Phabricator web
interface and stop any running Phabricator daemons (you can disable this
warning with --force).

    Are you ready to continue? [y/N] y

Storage is up to date. Use "storage status" for details.
Synchronizing static tables...
Verifying database schemata on "localhost"...
Found no adjustments for schemata.

Target                Error
phabricator_dashboard Missing
phabricator_daemon    Missing

 SCHEMATA ERRORS 

The schemata have errors (detailed above) which the adjustment workflow can
not fix.

If you are not developing Phabricator itself, report this issue to the
upstream.

If you are developing Phabricator, these errors usually indicate that your
schema specifications do not agree with the schemata your code actually
builds.
 ANALYZE  Analyzing tables...
Done.                                                                         
 ANALYZED  Analyzed 512 table(s).

After that, when I finished update (started daemons and httpd) my phabricator instance works properly. But even if you won’t reproduce this error, please give me at least a hint how to fix SCHEMATA ERROR, that this message won’t appear again

Reproduction Instructions
Try checkout on 4c242256e4, make the storage update, and then pull from stable and make it again
If this won’t help, here I put my reflogs which reflect the “upgrading” steps I’ve done:

f0f352ffd0 (HEAD -> stable, origin/stable) HEAD@{0}: pull: Fast-forward
4c242256e4 HEAD@{1}: pull: Fast-forward
3d481fb757 HEAD@{2}: pull: Fast-forward
61a5a48115 HEAD@{9}: checkout: moving from master to stable
5e94343c7d HEAD@{10}: clone: from https://github.com/phacility/phabricator.git

Here’s reflog for arcanist:

8b5fbb5a (HEAD -> stable, origin/stable) HEAD@{0}: pull: Fast-forward
feb5f4d4 HEAD@{1}: pull: Fast-forward
4d22e0f8 HEAD@{2}: pull: Fast-forward
ed5d02ab HEAD@{3}: checkout: moving from master to stable
eb732555 (master) HEAD@{4}: clone: from https://github.com/phacility/arcanist.git

And for libphutil:

7736d42 (HEAD -> stable, origin/stable) HEAD@{0}: pull: Fast-forward
b49ed9b HEAD@{1}: pull: Fast-forward
564c7b3 HEAD@{2}: pull: Fast-forward
a537ba0 HEAD@{3}: checkout: moving from master to stable
cad1985 (master) HEAD@{4}: clone: from https://github.com/phacility/libphutil.git

Phabricator/Arcanist Version
I think commit hashes say about version, don’t they?

Is this the first time you’ve run bin/storage upgrade?
The errors mean you’re missing 2 databases, one of which is critical for the home page, and the other for the daemons.

Have you been doing anything else to the database other than bin/storage upgrade?