You have upgraded recently to ShortPoint 6.2.X.X from 6.1.0.0 and you need to make sure the upgrade was successful and you followed the exceptional upgrade step as expected. Here are the steps you need to follow:

Step 1: Navigate to ComponentManifests list in App Catalog site collection

From your App Catalog site collection, you need to navigate to the backend list called Component Manifests. To go there, you need to go to below URL. 

<Your App Catalog Site Collection>/Lists/ComponentManifests 

For example, if your App Catalog site collection URL is https://myTenant.sharepoint.com/sites/Apps, please use below URL:

https://myTenant.sharepoint.com/sites/Apps/Lists/ComponentManifests

If you have an App Catalog site that is named something other than Apps, please make sure to update the URL:

https://myTenant.sharepoint.com/sites/<Your Custom App Catalog Site Name>/Lists/ComponentManifests

For example, if you site is named catalogApps:

https://myTenant.sharepoint.com/sites/catalogApps/Lists/ComponentManifests

Step 2: Make sure you have only one entry of ShortPointCustomActionsApplicationCustom component

In the list, you should see only one entry of ShortPointCustomActionsApplicationCustom 

However, if you see two entries of same extension, you need to delete the ShortPoint SPFx and Upload it again:

How to fix it?

To fix this issue, you need to perform same step again as explained here. You need not to do anything in your site collection where ShortPoint only installed, only delete the app and add again will fix the problem for you.