Cannot upload files to a specific Directory after the branch is merged with master

We’ve just installed and configured Gitlab CE on our Ubuntu server. So far, everything seems to be working fine except the file upload to a specific directory from Gitlab page.

Here is the issue in detail.
We’ve two branches for testing, Master and Develop.
Develop branch was cloned from Master.
Both Master and Develop branch have Documents directory.
We select Develop branch and then select Documents directory.
We then, click on the “+” sign and select Upload File wherein we place the place to be uploaded to “Documents” directory.
Upon clicking on upload button, the file for some reason gets uploaded to the parent directory of “Documents”. We expect that the word document file to be uploaded is saved to “Documents” directory.

We’re using self-managed gitlab and are on version 12.9.2

Please help as I don’t understand why it wouldn’t upload the file in the directory where it’s suppose to upload. Is there any limit on each of the directory created within the project?