Could it be that the rule "Source code should be indented consistently" does not work correctly when the source code contains tabs?
ID: squid:IndentationCheck
The warning says that the code must start at position 9 for instance, but the first character is actually at that position.
I now replaced the SonarQube rule with the Checkstyle rule and will see how this works. You deprecated the Checkstyle rule although it has much more options and possibly works better.