This article provides steps to determine if you have a bad port or if the port is not coming up due to another reason.

QFX5100 fpc0 et-0/2/0 >>> et-1/2/0 QFX5100 fpc1

Ports set as VC port, but not coming up.

The suggestion is to run layer 1 tests to determine if you have a bad port, and if you do, in which of the 2 devices you have it.

As VC port: 

To perform the test, you can set another ports as vc ports and move the connection. If you have an existing working connection, swap the non working connection with the working one and check if the port comes up.

We swapped the connections to the other available ports and the connection came up, we moved the connection fpc0 first to port et-0/2/1, port came up.

We then moved the port back to fpc0 et-0/2/0, and tried moving the fpc1 et-1/2/0 to et-1/2/1, port did not come up. Issue isolated to fpc0 port et-0/2/0.

We then proceeded to check the connection as a regular uplink port and not as virtual chassis port.

As ethernet port: remove the fec.
 

# set interfaces et-0/2/0 gigether-options fec none
# set interfaces et-1/2/0 gigether-options fec none

Same result, port in fpc0 did not come up, moving the connection to another makes it work fine.
Issue isolated to port in expansion module pic 2, proceeded to RMA the Expansion module.