I noticed a bug on the RB5009 where the 100/10 Mbps port indicator light isn't working.
I have one 100 Mbps port and another 10 Mbps port, but the indicator light on the router itself is green, indicating that the port is operating at Gigabit speed. However, the actual speed is 100 Mbps and 10 Mbps, respectively, because it's only using 4 wires instead of 8. My model is non-POE: RB5009UG+S+IN.
How can I resolve this issue?
It seems to work as expected. There's no bug here.
Read the manual maybe next time ¯\_(ツ)_/¯.
Welcome.
Bye.
That's what tech support answered 
This is expected behavior for RB5009UG+S-IN router. For this model, on Ethernet port 1 the orange LED indicates PoE-in status, but for Ethernet ports 2-8 the orange LED is unused: RB5009UG+S+IN | RouterOS Manual
In this case, the green LEDs on the Ethernet ports indicate link and activity, but not port speed.