Table key_value do not have a primary key.

key_value does have a primary key: 'primary key' => ['collection', 'name'].

I can't reproduce this on 10.1.x-dev. Table key_value has had a primary key for as long as it has existed.

You are right @cilefen. Line 318 in core/lib/Drupal/Core/KeyValueStore/DatabaseStorage.php. So it is our own problem. Our databases are not regular. Problem solves with sql command,
ALTER TABLE `<database>`.`key_value` DROP INDEX `collection`, ADD PRIMARY KEY (`collection`, `name`) USING BTREE;
No Drupal error message any more after that. Those databases come from D8 through D9.