If you have one version of your app on the desktop and another version of your app in the Applications folder, try this test ( and make sure they have different version numbers)
Run one version of your app from the desktop. Then double-click a document that loads into your app. What just happened? The app in the Applications folder just ran and opened your document. You now have two versions of your app running and the document loaded into the wrong app.
Seems like a serious bug to me. If an app is currently running and you double-click on a document that belongs to that app, the document should load into that currently running app. (That is the way all previous version of MacOs have worked)