You deal with them by checking that the values you found are actually solutions to the original equation. If you perform operations such as squaring both sides of an equation, there might be extraneous solutions, which won't be solutions of the original equation.
You shouldn't really have "missing" solutions, unless you do things like dividing both sides by a variable whose value could possibly be zero. For example, if you have the equation ##x^2 = x##, it is tempting to divide both sides by x, getting the equation x = 1. That's not the smartest way to solve this equation, though. It's better to rewrite it as ##x^2 - x = 0##, and then factor the left side to ##x(x - 1) = 0##, from which you can obtain both solutions.
Another example is the equation ##\sin(x) = \frac 1 2##. If you naively apply the function ##\sin^{-1}## to both sides, you end up with ##x = \frac \pi 6##. Doing this, you miss out on ##x = \frac{11\pi} 6##, not to mention an infinite number of other solutions.