Thanks for getting in touch. Just to make sure I understand your scenario correctly, you have a step in your deployment scenario that has the same role as your SD target but when the deployment runs it skips that target. Is that correct?
Could I check which step you are using? Both the Deploy a Service Fabric App and the Run a Service Fabric SDK PowerShell Script should be valid for Service Fabric targets.
Would you be able to attach a screenshot of the deployment process and the task log from a deployment to help us troubleshoot?