There are many Japanese words that use irregular kanji. I don't know why that is, but I feel like it's similar to learning irregular spellings in English -- why does T-H-R-O-U-G-H sound like threw? It just does. Why doesn't "rough" sound like "roux"? It just doesn't. That said, here's a link to an article that touches on this subject and might help you with your studies. Good luck! http://www.kanjiclinic.com/kc26final.htm

Originally, Kanji letters letters were brought by ancient China in 4th century to Japanese people, who had no letters. Of course, the pronunciations of the Kanji letters were not matched to Japanese ones. So, Japanese people began to use Kanji letters with two type of pronunciations, Chinese and Japanese.