V = d/t is an average velocity and you are plugging that value in for the final velocity. If you start at v=0 and finish at Vf, then Vavg is 1/2Vf. This means that Vf = 2Vavg, so you need to say that 2Vavg = at. That gives 2(d/t) = at which leads to d = 1/2at^2.
Whenever there is half in an equation that seems curious, it's usually the fact that it's an average value. That's where the 1/2 in PEspring = 1/2kx^2 comes from as well.