I observe the same effect on Asus P10S-M WS motherboard with Ubuntu
18.04, kernel 4.15.0-22-generic

(from lshw :)
product: P10S-M WS Series
vendor: ASUSTeK COMPUTER INC.
version: Rev 1.xx

description: BIOS
vendor: American Megatrends Inc.
version: 4401
date: 03/05/2018

'biosdevname -d' prints both (2) onboard interfaces with BIOS device:
em1

BIOS device: em1
Kernel name: eno1
Permanent MAC: 2C:FD:A1:C6:F3:FA
Assigned MAC : 2C:FD:A1:C6:F3:FA
ifIndex: 2
Driver: igb
Driver version: 5.4.0-k
Firmware version: 3.16, 0x800004d7
Bus Info: 0000:01:00.0
PCI name      : 0000:01:00.0
PCI Slot      : embedded
SMBIOS Device Type: Ethernet
SMBIOS Instance: 1
SMBIOS Label:  Onboard LAN
sysfs Index: 1
sysfs Label:  Onboard LAN
Embedded Index: 1

Duplicate: True
BIOS device: em1
Kernel name: rename3
Permanent MAC: 2C:FD:A1:C6:F3:FB
Assigned MAC : 2C:FD:A1:C6:F3:FB
ifIndex: 3
Driver: igb
Driver version: 5.4.0-k
Firmware version: 3.16, 0x80000513
Bus Info: 0000:02:00.0
PCI name      : 0000:02:00.0
PCI Slot      : embedded
SMBIOS Device Type: Other
SMBIOS Instance: 1
SMBIOS Label:  Onboard 1394
sysfs Index: 1
sysfs Label:  Onboard 1394
Embedded Index: 2

Duplicate: True


so, this is not limited to SUpermicro boards only

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https://bugs.launchpad.net/bugs/1578141

Title:
  Predictable interface names partially broken with igb driver

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