There is a bug in DefinitionMergeService (part of auto-export) that results in nonsense warnings about defining a property with the same value in multiple source files, and then listing the same source file multiple times. This is due to an underlying bug in how DMS updates the configuration model incrementally during auto-export. Note that this doesn't appear to have any bad outcome other than the unnecessary warnings, since the configuration model is fully rebuilt at the very end of the auto-export cycle, and the specific error in the incremental update doesn't have a significant effect.
This bug can be reproduced intermittently by adding the banner component from Essentials to a new archetype-generated project. It appears to be timing dependent, so the warnings are not always produced.