Suppose we have two curves given by: $$r=20sin2\theta $$ $$r= 20 cos2\theta$$
Now by solving the equations, we get the solution as $\theta = \frac{\pi}{8}$.
However, on graphing the equations, I can find 8 points of intersection . Where could I have done a mistake?

You have to take into account two issues. One of them is the periodicity of the $\tan$ function. $\tan(2\theta)$ has a periodicity of $\pi/2$, so you get $\pi/8, 5\pi/8, 9\pi/8, 13\pi/8$ as possible solutions in the $[0,2\pi)$ interval. The other issue to consider is that the $r$ in the two equations is not necessarily the same. You also get solution if $r_1=-r_2$ and $\sin(2\theta)=-\cos(2\theta)$. From the definition of $\arctan$ you get $\theta=-\pi/8$, which yields $3\pi/8, 7\pi/8, 11\pi/8, 15\pi/8$ in the above mentioned interval.