I have a similar problem.

It first occurred with the kernel upgrade to 3.2.0-64 (I guess) and a
Seagate USB 3.0 external HD.

Now I bought a WD Passport ultra harddrive. Same issue:

The WD Passport Ultra harddrive works without problems on a USB 2.0
port, yet when connected to an USB 3.0 port, dmesg shows the following
error:

[  887.802679] usb 4-1: new SuperSpeed USB device number 2 using xhci_hcd
[  887.819755] scsi10 : usb-storage 4-1:1.0
[  888.815996] scsi 10:0:0:0: Direct-Access     WD       My Passport 0820 1007 
PQ: 0 ANSI: 6
[  888.816292] scsi 10:0:0:1: Enclosure         WD       SES Device       1007 
PQ: 0 ANSI: 6
[  888.817656] sd 10:0:0:0: Attached scsi generic sg2 type 0
[  888.817888] ses 10:0:0:1: Attached Enclosure device
[  888.817994] ses 10:0:0:1: Attached scsi generic sg3 type 13
[  919.523155] usb 4-1: reset SuperSpeed USB device number 2 using xhci_hcd
[  919.536526] xhci_hcd 0000:05:00.0: xHCI xhci_drop_endpoint called with 
disabled ep ffff880306f35e00
[  919.536531] xhci_hcd 0000:05:00.0: xHCI xhci_drop_endpoint called with 
disabled ep ffff880306f35e40

uname -a

Linux jb-desktop 3.2.0-67-generic #101-Ubuntu SMP Tue Jul 15 17:46:11
UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

lsusb -vvv

[...]
Bus 004 Device 002: ID 1058:0820 Western Digital Technologies, Inc. 
Couldn't open device, some information will be missing
Device Descriptor:
  bLength                18
  bDescriptorType         1
  bcdUSB               3.00
  bDeviceClass            0 (Defined at Interface level)
  bDeviceSubClass         0 
  bDeviceProtocol         0 
  bMaxPacketSize0         9
  idVendor           0x1058 Western Digital Technologies, Inc.
  idProduct          0x0820 
  bcdDevice           10.07
  iManufacturer           1 
  iProduct                2 
  iSerial                 5 
  bNumConfigurations      1
  Configuration Descriptor:
    bLength                 9
    bDescriptorType         2
    wTotalLength           44
    bNumInterfaces          1
    bConfigurationValue     1
    iConfiguration          4 
    bmAttributes         0x80
      (Bus Powered)
    MaxPower              224mA
    Interface Descriptor:
      bLength                 9
      bDescriptorType         4
      bInterfaceNumber        0
      bAlternateSetting       0
      bNumEndpoints           2
      bInterfaceClass         8 Mass Storage
      bInterfaceSubClass      6 SCSI
      bInterfaceProtocol     80 Bulk-Only
      iInterface              6 
      Endpoint Descriptor:
        bLength                 7
        bDescriptorType         5
        bEndpointAddress     0x81  EP 1 IN
        bmAttributes            2
          Transfer Type            Bulk
          Synch Type               None
          Usage Type               Data
        wMaxPacketSize     0x0400  1x 1024 bytes
        bInterval               0
        bMaxBurst              15
      Endpoint Descriptor:
        bLength                 7
        bDescriptorType         5
        bEndpointAddress     0x02  EP 2 OUT
        bmAttributes            2
          Transfer Type            Bulk
          Synch Type               None
          Usage Type               Data
        wMaxPacketSize     0x0400  1x 1024 bytes
        bInterval               0
        bMaxBurst              15

[...]
Bus 004 Device 001: ID 1d6b:0003 Linux Foundation 3.0 root hub
Couldn't open device, some information will be missing
Device Descriptor:
  bLength                18
  bDescriptorType         1
  bcdUSB               3.00
  bDeviceClass            9 Hub
  bDeviceSubClass         0 Unused
  bDeviceProtocol         3 
  bMaxPacketSize0         9
  idVendor           0x1d6b Linux Foundation
  idProduct          0x0003 3.0 root hub
  bcdDevice            3.02
  iManufacturer           3 
  iProduct                2 
  iSerial                 1 
  bNumConfigurations      1
  Configuration Descriptor:
    bLength                 9
    bDescriptorType         2
    wTotalLength           31
    bNumInterfaces          1
    bConfigurationValue     1
    iConfiguration          0 
    bmAttributes         0xe0
      Self Powered
      Remote Wakeup
    MaxPower                0mA
    Interface Descriptor:
      bLength                 9
      bDescriptorType         4
      bInterfaceNumber        0
      bAlternateSetting       0
      bNumEndpoints           1
      bInterfaceClass         9 Hub
      bInterfaceSubClass      0 Unused
      bInterfaceProtocol      0 Full speed (or root) hub
      iInterface              0 
      Endpoint Descriptor:
        bLength                 7
        bDescriptorType         5
        bEndpointAddress     0x81  EP 1 IN
        bmAttributes            3
          Transfer Type            Interrupt
          Synch Type               None
          Usage Type               Data
        wMaxPacketSize     0x0004  1x 4 bytes
        bInterval              12
        bMaxBurst               0


** Changed in: linux (Ubuntu)
       Status: Incomplete => Confirmed

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https://bugs.launchpad.net/bugs/1337196

Title:
  3.2.0-64 kernel version breaks usb3.0 port in asus k53sv

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