Upload finished but only partialy files uploaded

Hi, 

We've been experiencing an upload issue recently while uploading many folders in bulk. 

for example. we are uploading 10 folders with 1000 files. 100 files/folder. 

The upload was finished, and 10 folders were created, but only some of the folders had files inside them. The final result will be 10 folders and 300s files. most of the created folders are empty.

We have checked our firewalls, and tested on many computers and can't get different results.