Finding "the root of a problem" means finding the basic cause, or origin of something. A square number is a number multiplied by itself. We see the words "square" and "root" in the joke. The square root is a number which produces a quantity when multiplied by itself. The joke is circled around the word "root" and how it can create "square root" and also fit into the saying "the root of the problem". 
In equations with square numbers I can never find the root of the problem .