In the MyFileGateway UI on the upload tab you have three options:
1) Choose the mailbox path
2) Select the file which should be uploaded
3) Rename the file
The third options is not mandatory.
From your point of view there should be a setting where you can fade out or disable the renaming of a file.
Many of our partners (even English native speakers) are using this field for notes. Then the filename will be changed to this string, mostly without any file extension.