Hi @jarryd,
Thanks for asking this here! 
If you use our fastlane step that does not change any configuration or any file in your repository. All it does is it updates the installed fastlane (if required, based on the inputs you provide) and then runs the fastlane ... command. That’s pretty much all. You can also see the fastlane command it runs in the log.
If the wrong target is selected I think that’s because of a configuration which is not committed into your repository, or maybe a fastlane bug.
Can you please follow this guide How to debug your build locally / "It works on my Mac/PC but not on bitrise.io" ? That should help you to reproduce the issue on your own Mac.
Let us know how it goes or if you have any questions!