The answer to your question is really quite simple. God said that what He created was very good indeed (or really good, or better than good) prior to the fall of man and woman.
With the fall of our first parents, both they and the world they inhabited were spoiled permanently. Paul wrote that
". . . the creation was subjected to futility, not willingly, but because of Him who subjected it, in hope that the creation itself also will be set free from its slavery to corruption into the freedom of the glory of the children of God. For we know that the whole creation groans and suffers the pains of childbirth together until now" (Romans 8:20-22 NASB Updated Version).
That spoliation became worse and worse, to the point where God "repented" of His having created humans in His image. Remember, the Bible tells us that humanity had become so depraved that
". . . every intent of the thoughts of his heart was only evil continually" (6:5).
Think of the "absolute" terms in that verse:
and evil continually
This may sound flip, but if I were God, I would've wanted to
". . . 'blot out man whom I have created from the face of the land, from man to animals to creeping things and to birds of the sky; for I am sorry that I have made them.'"
The good news, however, comes in verse 8, which is certainly a pivotal verse in Genesis:
"BUT Noah found favor in the eyes of the LORD."
In conclusion, what God created good, man spoiled. There is no contradiction between these two facts.
Take a homely analogy. Cancer is ravaging a person's intestinal tract. The only recourse is to remove the cancerous intestines and transplant into the body of the cancer patient the healthy intestines from an organ donor who has just died. Is the transplant cruel or unfair, or does it contradict the Hippocratic Oath in any way? Of course not. Out with the diseased body part, and in with the healthy body part, to give the cancer survivor a new lease on life. He or she will still die, but their life could be extended for many years.