Hi. That sounds like the difference between a metadata format project (src) and a source format project (force-app/main/default).
How are you creating the project? I’m assuming you’re creating it from version control? If so, IC should recognize it as being a source format project based on the presence of sfdx-project.json in the project root, and you’ll be required to use a CLI-managed connection with the project.
Regards,
Scott Wells