thanks for the hints @tkaiser
I tried to reinserting the cable a few times, but nothing changed. I also tried another cable.
I also looked at the connections on cable and ports, they seem to look fine.
When I connect the device to my linux machine it works as expected.
Here is the dmesg output of the orange pi lite2 with kernel Linux 3.10.65,
with the image from orangepi Ubuntu Server from 2018-03-12
[12307.950096] usb 5-1: new high-speed USB device number 4 using xhci-hcd
[12308.001036] usb 5-1: New USB device found, idVendor=125f, idProduct=a37a
[12308.001063] usb 5-1: New USB device strings: Mfr=1, Product=2, SerialNumber=3
[12308.001081] usb 5-1: Product: USB
[12308.001098] usb 5-1: Manufacturer: JMicron
[12308.001115] usb 5-1: SerialNumber: DD564198838738739F
[12308.030823] usb-storage 5-1:1.0: USB Mass Storage device detected
[12308.031067] scsi2 : usb-storage 5-1:1.0
[12309.030858] scsi 2:0:0:0: Direct-Access INTEL SS DSCKKW512G8 3203 PQ: 0 ANSI: 6
[12309.032869] sd 2:0:0:0: [sda] 1000215216 512-byte logical blocks: (512 GB/476 GiB)
[12309.033347] sd 2:0:0:0: [sda] Write Protect is off
[12309.033372] sd 2:0:0:0: [sda] Mode Sense: 47 00 00 08
[12309.033823] sd 2:0:0:0: [sda] Write cache: enabled, read cache: enabled, doesn't support DPO or FUA
[12309.042505] sda: sda1 sda2
[12309.045850] sd 2:0:0:0: [sda] Attached SCSI disk
on my linux machine it looks correct with kernel Linux 4.4.0-116-generic
lsusb -t
/: Bus 04.Port 1: Dev 1, Class=root_hub, Driver=xhci_hcd/6p, 5000M
|__ Port 1: Dev 3, If 0, Class=Mass Storage, Driver=uas, 5000M
|__ Port 2: Dev 2, If 0, Class=Mass Storage, Driver=usb-storage, 5000M
/: Bus 03.Port 1: Dev 1, Class=root_hub, Driver=xhci_hcd/8p, 480M
|__ Port 3: Dev 2, If 0, Class=Hub, Driver=hub/4p, 480M
|__ Port 4: Dev 3, If 0, Class=Hub, Driver=hub/4p, 480M
|__ Port 1: Dev 4, If 0, Class=Human Interface Device, Driver=usbhid, 1.5M
|__ Port 1: Dev 4, If 1, Class=Human Interface Device, Driver=usbhid, 1.5M
/: Bus 02.Port 1: Dev 1, Class=root_hub, Driver=ehci-pci/2p, 480M
|__ Port 1: Dev 2, If 0, Class=Hub, Driver=hub/4p, 480M
/: Bus 01.Port 1: Dev 1, Class=root_hub, Driver=ehci-pci/2p, 480M
|__ Port 1: Dev 2, If 0, Class=Hub, Driver=hub/4p, 480M
[906487.979366] usb 4-1: new SuperSpeed USB device number 3 using xhci_hcd
[906487.996183] usb 4-1: New USB device found, idVendor=125f, idProduct=a37a
[906487.996192] usb 4-1: New USB device strings: Mfr=1, Product=2, SerialNumber=3
[906487.996197] usb 4-1: Product: USB
[906487.996202] usb 4-1: Manufacturer: JMicron
[906487.996207] usb 4-1: SerialNumber: DD564198838738739F
[906487.998450] scsi host7: uas
[906487.999145] scsi 7:0:0:0: Direct-Access INTEL SS DSCKKW512G8 3203 PQ: 0 ANSI: 6
[906488.000287] sd 7:0:0:0: Attached scsi generic sg3 type 0
[906488.000428] sd 7:0:0:0: [sdd] 1000215216 512-byte logical blocks: (512 GB/477 GiB)
[906488.000439] sd 7:0:0:0: [sdd] 4096-byte physical blocks
[906488.001004] sd 7:0:0:0: [sdd] Write Protect is off
[906488.001013] sd 7:0:0:0: [sdd] Mode Sense: 53 00 00 08
[906488.001319] sd 7:0:0:0: [sdd] Write cache: enabled, read cache: enabled, doesn't support DPO or FUA
[906488.005007] sdd: sdd1 sdd2
[906488.006719] sd 7:0:0:0: [sdd] Attached SCSI disk
Does somebody else has the same problem with the lite 2 or does usb 3 work?. Not sure if its a driver/software problem or hardware. I will try the android image next.