Greetings @bengur,
How are you deploying your new container images? Are you just deploying the OSTree over network? If so that won’t work because container images are not managed by OSTree.
As stated in the article here: Pre-provisioning Docker Containers onto a Torizon OS image | Toradex Developer Center
To deploy your custom image with custom containers you must use Toradex Easy Installer to flash the image whole.
Best Regards,
Jeremias