I can only guess the Zcontroller in the corner is how you are powering? What power brick or version is that?
Second part is, MTH has not posted a parts diagram of that specific car, however I know that some used switching mode regulators, and others used linear regulators.
Example switching regulator
VS
Linear style regulator
One theory is that a chopped AC power waveform might interact with the switch mode style supply.
The LEDS are simply powered by 6V and then strands or the light strings are current limited with a resistor.
I would say return it, but given demand and supply- hopefully the dealer can exchange for you.
Remember, this whole "repair" and warranty is more like refund and you end up car or train less. There is no MTH factory service center, there is no warehouse with spare cars. That means it really matters who the dealer is, are they a service center, did they stock parts and do this level of repair?