Are you referring to the powerbase?
I am assuming so as only it and the controllers themselves have lights.
A flashing light inidicates an overload.
This is usually caused by a short circuit which again is usually caused by metal braid on the track.
Unplug and remove the powerbase form the layout and use a vacuum cleaner to ensure there is no metal on the track.
Plug the powerbase back in and it should turn green after a few moments.
If it turns red and blinks there is a problem with the powerbase and/or the power supply (power adapter).
They will need replaced: Please contact Sclaextric Customer Care at the right.
If it stays green but turns red when the trigger is pulled or when a car is set on the track then there is something wrong with the cars. Possibly a loose wire is causing a short in the car.
(if you are savvy with electronics you can use an Ohm-meter to test all this).
If there is no obvious problem with the cars then the powerbase likely has a fault and needs replacing I am afraid.