You simply call the scatter function twice, matplotlib will superimpose the two plots for you. You might want to specify a color, as the default for all scatter plots is blue. This is perhaps why you were only seeing one plot.
import numpy as np
import pylab as plt
X = np.linspace(0,5,100)
Y1 = X + 2*np.random.random(X.shape)
Y2 = X**2 + np.random.random(X.shape)
plt.scatter(X,Y1,color="k")
plt.scatter(X,Y2,color="g")
plt.show()
