For example YAML configuration contains deprecations, f.e. config_dev.yml contains non-escaped expressions:

monolog:
    handlers:
        main:
            type: stream
            path: %kernel.logs_dir%/%kernel.environment%.log
            level: debug
            channels: [!event]
        console:
            type: console
            process_psr_3_messages: false
            channels: [!event, !doctrine, !console]

In the web panel you can see notices like Using the unquoted scalar value "!event" is deprecated since version 3.3 and will be considered as a tagged value in 4.0.. But when you run functional tests there are no notices, tests are passed. You can only see serialized deprecations in the var/cache/test/appTestDebugProjectContainerDeprecations.log. It happens because errors are caught at https://github.com/symfony/symfony/blob/master/src/Symfony/Component/HttpKernel/Kernel.php#L464 and previous PHPUnit Bridge handler is not called.