This is expected behavior when targeting UltraScale and UltraScale+ devices.
This is because in most conditions the transceiver is able to detect both the 12G-SDI integer line rate and the fractional line rate with a single reference clock.
(Note: Users should use both reference clocks to guarantee that that the GT CDR does operate within spec and will be able to lock in all conditions.)
Because the SMPTE UHD-SDI RX Subsystem is able to find the TRS and perform successful alignment with the 12G-SDI integer line rate mode, it is not moving to scan the 12-G SDI fractional line rate mode.
In this case the rx_mode is set as 3b101 even though 12-G SDI fractional line rate data is received.
The rx_bit_rate generated by the UHD-SDI Compact GT Wrapper correctly reflects the 12G-SDI integer vs fractional line rates.
You should monitor the user rx_mode output and rx_bit_rate to determine if the incoming signal is 12G-SDI integer or fractional line rate.