You're copying a lot of stuff in same time and computer performance just dies. Try for example to copy 10+ ISO images same time.
There's QoS in networking, affinities and priorities in CPUs, but is there anything for hard drives to throttle I/O queues? Virtual filesystems? OS drivers?
Of course you can go around with this with for example
- Making list of files to copy and running script which copies files one by one
- Using software like TeraCopy
Windows and GNU/Linux solutions are welcome.