EMC Testing, Radiated Emissions
As far as I understand you have switching power supply that has unwanted emission. 
Your switching power supply is locked on the 500KHz and is generating 3V/2.5A output.

One of the confirmed methods in reducing the radiated EMI is using spread spectrum clock instead of the fix one (that in this case is 500KHz). If you simply could add some jitter to the clock (e.g. 500KHz +/- 20KHz) the concentration of the radiated energy will distributed over a wider range and the overall radiated energy of the switching device will be reduced.
There is an IEEE article that may could be helpfull
https://ieeexplore.ieee.org/document/1031552
Spread spectrum clock generation is very effective in reducing conductive radiation in micro controller based circuits too and some Freescale uCs have built-in SSCG engine.

There are some other ways. If your PCB had enough space, you could implement twisted pair on the PCB for line input and the same for line output.(some us patent exists for implementing twisted pair on PCBs)
You may have a big inductor on your circuit some are shielded and some are not. In your case using shielded inductor is much better. If you had any control on reducing the rise time of the 500KHz signal, It could be also effective on the radiation.