The problem here is mainly notational. There is only one solution to $x=\sqrt9$, which comes from the way that the square root function is defined. We often learn in grade school that $\sqrt x$ is defined as "the number whose square is equal to $x$", but this definition is incomplete: the square root function is defined as the ''positive'' number whose square is equal to $x$. As a result, even though $3^2=9$ and $(-3)^2=9$, it is incorrect to say that $\sqrt9=-3$. Mathematicians could have defined the square root function to map a number to both its positive and negative square roots (in other words, a function that maps a number to an ordered pair of numbers) but they did not.
As a side note, your manipulation of the equation $x^2=9$ to $x=\sqrt9$ is an example of what is known as an "extraneous solution." These kinds of solutions can crop up whenever you try to prove a statement in reverse, by starting with what you want to prove and manipulating it until you get a statement of fact. Whenever you prove something this way, there are some functions (including $\sqrt$) which may get you an answer with no real meaning. In other words, be careful whenever you try to do backwards proofs!
Hope this helps.
Also I've got some understanding for the square root functions now, thanks for all the clear explanations guys.
– Arvin Dec 08 '22 at 17:10