This is on current master I can't reproduce this using 1.4.3. I guess it relates to the stale auto redraw handling?

from mpl_toolkits.mplot3d import Axes3D


fig = plt.figure(figsize=(6.5,5.5))
ax = fig.add_subplot(1, 1, 1, projection='3d')
xs = np.random.rand(10)
ys = np.random.rand(10)
zs = np.random.rand(10)
ax.set_aspect('equal')

ax.scatter(xs, ys, zs)
ax.set_xlim(0,1)
ax.set_ylim(0,1)
ax.set_zlim(0,1)
fig.tight_layout()

results in

Rotating the figure restores the correct axes. I can't reproduce it with QT5Agg or GTK3Agg

It seems like both the equal axis z and the original z axis are drawn on top of each other. It doesn't seem to happen in regular 2D plots.