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No, this is expected.

/opt/ros/indigo/stacks is added for backwards-compatibility reasons: in earlier versions of ROS, that is where all content of packages was placed (distributed in stacks, hence the name). As there could still be some old packages that depend on artefacts to be located there, the directory is still added to the package search path.

Note that even though the directory is added to the search path, whether it actually exits on your FS depends on whether you have installed any package that places artefacts there.