No files listed with "Include subfolders" checked

Modify the "List View Threshold" may solve this issue because it exceeded the maximum limit. Please check the two parts below:

List View Threshold:

1. Go to Central Administration -> Application Management
2. Select a desired web application, then click on ‘General Settings’ on the ribbon and select ‘Resource Throttling’, and change the settings below:

Upload Size:

1. Go back to General Settings in the ribbon, select ‘General Settings’ option
2. Scroll down to the bottom, set the desired maximum upload size:

This solution also applies to the issue that after uploading documents, the page won’t redirect to the check in page.