I had exactly this problem. I normally use MSC and all my files were originally transferred to the View in this mode - than the problem occurred with the multiple entries. Refreshing helped sometimes to solve it for a while but the same files (!) kept doubling and even worse (10 times the same entry!).

So, the solution that works now 100 % with my View was to change the MTP-mode and to transfer the files that kept changing to the view in this mode. Afterwards, I change back to my preferred MSC-Mode (& delete the corresponding MSC-Files). Well, now are not all the files & folders visible at the same time when connected to the PC but this doesn’t disturb me at all and the View shows all the files as single entries – as it should be and I can use the MSC-mode.