The problem is that the protection diode is on the same side as the series resistor.
Consider for example if there is 10V input voltage. Then the FPGA diodes will start clamping at 3V (koti.kapsi.fi/jpa/stuff/pix/dso_ … urrent.png). Because the voltage is clamped at 3V, absolutely no current will flow to the 5V protection diode. Such a diode is completely useless, it won’t do anything until the FPGA input is already broken.
I’m not sure if 3.3V protection diodes would be effective either. The FPGA input diode forward voltage will probably rise a bit when the current rises, so it might still help something.
Optimal solution might be replacing the R41 and R42 with a series connection of two resistors, with the clamp diode in between them. But this is probably quite difficult to do.