MDIO behaviour in the provided trace is valid.
Please check MDC to MDIO delay tMDKHDX controlled by the MDIO_CFG[MDIO_HOLD].
Please check whether MDIO_CFG[NEG]=1 then LS1043A will transmit data on falling edge of the clock.
This implies with MDIO_CFG[NEG]=1 the tMDKHDX should be measured with respect to the falling edge of clock.
> can I configure the CPU to use falling edge sampling?
No.