If I solve the parabola: $y^2=4ax$ and the circle: $x^2+y^2=\frac{9a^2}{4}$ I get a quadratic in $x$; ie: $$4x^2+16ax-9a^2=0$$ which has roots $x=\frac{a}{2},-\frac{9a}{2}$. But if we see the graphs of these two, both the intersections occur at same $x$-coordinate so why does this extra root $x=-\frac{9a}{2}$ come?
So my question is that if the circle was unknown say $x^2+y^2=b^2$ then I would have put the discriminant of the quadratic in $x$ as $0$ but that would be wrong so how do I judge that an extraneous root will be present and discriminant won't be zero?
Basically when you combine the two equations, you have the implication that a solution of the two equations is also a solution of the combined equation but not necessarily the other way round! In this case you lose the information that $4ax\geq0$ which is implicitely given in the equation of the parabola.
edit: With regards to your second question. If you substitute $y^2$ you will always end up with 2 distinct roots for the $x$-equation regardless of the value of $b$ (unless $a=b=0$). It really depends on your choice of how you tackle the problem. E.g. if you substitute for $x$ (not that I would personally recommend it) you get a forth order equation: $$\frac{y^4}{(4a)^2}+y^2=\frac{9a^2}{4}$$ which yields the two real solutions for $y$ you want. That's why it is so important to doublecheck solutions after a computation and go back to the original problem.