Explanation of the error:
This Salesforce error "CustomApplication - You specified one or more duplicate ProfileActionOverride values.", is shown because there are duplicate values of ProfileActionOverride present in the XML.
Often times there are so many duplicates that you may need to edit the XML in one of the ways as mentioned below to find the duplicates and remove them.
Copy the XML from diff viewer in the comparison.
Search Google for an XML to CSV converter.
Paste the XML and remove the lines just below the first line until the
<profileActionOverrides>starts and same in the end of the XML as well. Click convert.
After converting, open it using an Excel/Google sheet.
We have selected Google sheets and then selected
Split text to columnsto separate the items as shown above.
After separating, we have selected
Data clean-up - Clean-up suggestions
This is showing me the duplicates which were causing the issues.
Once done, you can convert this back from CSV to XML using a converter.
Once the duplications have been found you have 2 options.
Remove the duplicate XML directly in your repo.
Follow this guide on how to change the deployment package, to remove any of those duplicates.
Further examples of this Salesforce validation error can be found here: