Ethernet 25 MHz and 50 MHz harmonics cuases radiation emission during the EMC lab test
You're going to have to debug it. 

First, how much over the emission limit are you?

Second, is there significant 25MHz noise on the supplies? If you're lucky you may simply have to decouple them better.

Third, which signals are radiating most? For example, if you lift TXP,TXN at the PHY, does the noise go away? (Alternatively if you have software means to disable bits of the PHY, that can save some knife/solder work)

Fourth, when you find the culprit you have to remedy it. For example, screening around the TXD/RXD traces, or ferrite chokes on them, or improve their terminations, or provide current return paths from termination to the PHY chip.