=> I had problems with a large USB 3.0 (3TB and over) external hard-drive.
=> I have ext3 file system on a drive and I had a single partition for the entire drive.
Initially, when the data on the drive was less it would mount (and read/write) fine.
When the drive disk space was used up over 70%, I saw that the external hard drive would not mount when connected via the USB 3.0 port.
dmesg would show something like this:
[ 222.828893] xhci_hcd 0000:00:14.0: OUT Endpoint 02 Context (ep_index 03):
[ 222.828898] xhci_hcd 0000:00:14.0: @ffff8800d50bb080 (virt) @d50bb080 (dma) 0x000001 - ep_info
[ 222.828903] xhci_hcd 0000:00:14.0: @ffff8800d50bb084 (virt) @d50bb084 (dma) 0x2000016 - ep_info2
[ 222.828914] xhci_hcd 0000:00:14.0: @ffff8800d50bb088 (virt) @d50bb088 (dma) 0xd50d4401 - deq
[ 222.828918] xhci_hcd 0000:00:14.0: @ffff8800d50bb090 (virt) @d50bb090 (dma) 0x000000 - tx_info
[ 222.828926] xhci_hcd 0000:00:14.0: @ffff8800d50bb094 (virt) @d50bb094 (dma) 0x000000 - rsvd[0]
[ 222.828933] xhci_hcd 0000:00:14.0: @ffff8800d50bb098 (virt) @d50bb098 (dma) 0x000000 - rsvd[1]
[ 222.828941] xhci_hcd 0000:00:14.0: @ffff8800d50bb09c (virt) @d50bb09c (dma) 0x000000 - rsvd[2]
[ 222.829004] xhci_hcd 0000:00:14.0: Endpoint 0x81 not halted, refusing to reset.
[ 222.829009] xhci_hcd 0000:00:14.0: Endpoint 0x2 not halted, refusing to reset.
[ 222.829016] usb_reset_device returns 0
[ 222.829023] scsi command aborted
[ 222.829028] *** thread sleeping
[ 222.829079] scsi 8:0:0:0: Device offlined - not ready after error recovery
[ 222.829144] usb-storage 3-2:1.0: scan complete
[ 222.923625] xhci_hcd 0000:00:14.0: xhci_hub_status_data: stopping port polling.
However it mounted fine when connected via USB 2.0 ports
=> To understand the issue more I complied my kernel from source and enabled CONFIG_DYNAMIC_DEBUG, CONFIG_USB_DEBUG and few other flags that I don't remember now.
However, I couldn't get to spending more time on understand the xhci subsystem, so I don't yet know what might be happening.
=> But, I guess, one thing you could do is check if the issues are happening when connected via a USB 2.0 port too.
If things seem to be working via USB 2.0 then it might be a issue with the xhci subsystem.