Some but not all rail junctions will show a green box suggesting that it is a valid signal placement, but upon placing the signal it flashes the green/yellow/red error indicating the placement is invalid. The same issue occurs with chain signals.
An example of what the rail planner shows. The two invalid placements are circled.
This is the result of placing a signal on the "suggested" invalid location box. The signal shows invalid location error lights.
This is the result of normal, valid signal placement on the same junction.