If every positive number has two square roots and you can find the length of the side if a square window by finding a square root of the area, why is there only one answer for the length of a side?

Mathematically, there are always two answers, and one of them is always

negative. When you're making real windows with real wood and tools and

glass, there's no such thing as negative length, and you ignore the answer

that has no physical significance in the real world of screws and glue.