I have come across a web application project on GitHub that uses AGPLv3 as it's primarily licensed, but a sub-folder of the project is provided under a proprietary license. This contains the code for certain "enterprise"/paid-for features. This sub-folder is not dual-licensed, just provided under a custom proprietary license (Preventing production use).
As far as I can tell from looking at the code, since I have not downloaded & built the application, the AGPLv3 portion appears to rely on the sources in the proprietary sub-folder.
I respect that they can license code as they'd like, being the copyright holder, but is such a required proprietary section compatible with the freedoms provided in the AGPLv3? I'm not sure how the AGPLv3 applies to the application as a whole vs as parts of source code.
Reading the AGPLv3, this looks most relevant (Section 7, paragraph 1):
If additional permissions apply only to part of the Program, that part may be used separately under those permissions, but the entire Program remains governed by this License without regard to the additional permissions.
Based on that you could argue the AGPLv3 would apply to that sub-folder, being part of "the entire Program", but it could also be argued that everything but the proprietary section was provided as "the entire Program", albeit an incomplete one. If it provides context, the application is actively marketed as "Open Source".