By default, the queries are not filtered by View permissions. However, there is a configuration setting to enable FilterQueriesByViewPermissions globally for all data providers, or set it per provider overriding the default value. More information could be found in the following KB article
It is also possible to enable this behavior on a specific provider (e.g. LibrariesProvider since you are using documents and libraries):
Navigate through the main menu Administration -> Settings -> Advanced, Scroll to the Libraries node -> Providers -> OpenAccessDataProvider (or any other provider you are using to retrieve your files) -> Parameters, click "Create new", set the Key field to "filterQueriesByViewPermissions" (without quotes) and the Value field to "true" (without quotes) and Save changes.
Then reset your system and see if the permissions are being applied correctly.
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