Handling of modules and indexing of files has evolved since 5.6.x, so it’s possible that your configuration went through the cracks in older versions, and that latest 6.7.x is more cautious.
I would suggest you review the debug logs of your analysis, and understand which file paths are being treated by the scanner, and why are some paths seemingly indexed twice.
Note that I’ve observed such error in some cases where a broad sonar.sources was set either via command line and/or in one of the configuration files, which would override some of the scanner’s behaviour and/or create some overlap. A possible reason here is that. Double-check that on your end, and make sure to review both configuration on CI side and also on the scanner/project side.