iWork documents (Pages, Numbers, Keynote) on Mac can be saved as a "Single File" or as a "Package". Packages are folders that Mac OS interprets as a single file. If you save an iWork document (e.g., Keynote) as a Package and upload it to Egnyte, it will be uploaded as a folder.
If you see a "Show Package Contents" option when you right-click on a file, that means it's a Package and will be seen as a folder in Egnyte.
In order to resolve this issue, change the file type to a Single File from the File menu. Refer to the following screenshot for instructions.