We happened to encounter the same analysis warning after upgrading to 7.9.2 LTS.
Clone with a reference was detected. Some files will miss SCM information. This will affect features like auto-assignment of issues. Please configure your build to not clone using a local reference.
This was not an issue with 7.6, which we upgraded from. So this is definitely something that changed in 7.9.2.
We are currently using TeamCity 2018.1.3, and for us the fix was simply to add the build configuration parameter teamcity.git.useAlternates and set it to false (it’s true by default). The only documentation I was able to find regarding this setting was in a JetBrains community post here: https://teamcity-support.jetbrains.com/hc/en-us/community/posts/206831685-teamcity-git-use-local-mirrors-vs-teamcity-git-useAlternates
An alternative is probably to use a VCS root that has the Enable mirrors option not checked (it’s checked by default).