Upgraded FME FLOW to 2026.3: Worspace apps with file uploads only accepts some files

I have a set of workspace apps on our Flow to convert data between file formats. After upgrading our installation in test, I experience some strange behaviour: While uploading data to convert, some files are accekted, while others are rejected. 

Looking into the network data using the developer tools, I find that the accepted files gives a response like this:

{"serviceResponse": {
   "statusInfo": {"status": "success"},
   "session": "3cc570c6-2d66-4d66-86af-22c6a2f56696",
   "files": {
      "path": "",
      "file": [
         {
            "size": 1531,
            "name": "file name.kof"
         }
      ],
      "folder": [{"name": ""}]
   }
}}

The rejected files gives this response:

<html>
    <head>
        <title>Request Rejected</title>
    </head>
    <body>
        The requested URL was rejected. Please consult with your administrator.<br>
        <br>
        Your support ID is: 12358467762813340<br>
        <br>
        <a href='javascript:history.back();'>[Go Back]</a>
    </body>
</html>

Have anyone experienced this? Any tips on what could be causing this? 

I see this on several workspaces with different input file formats