There can definitely be more than one conflict in a story. In fact, novels usually have a bunch of them!
Conflicts can be either internal or external. An internal conflict is an inner struggle the character has, usually about a fear or making a decision. External conflicts, on the other hand, are problems the character has with outside influences.
The main conflicts in the story are internal. Both boys are struggling with the inadequacies of their own bodies or minds. In other words, Max has to learn to deal with being “slow” and Kevin has to learn to deal with not having a body that works. The external conflicts are between Max and Kevin and the bullies.
max has to deal with being slow
Man vs. man: Max vs. the bullies, then later his father who escapes from prison and kidnaps him.
Man vs. society: Both Kevin and Max have disabilities that has adverse affects on how others see them. The community sees Max as a danger to them, which has been unfounded.
Man vs. Nature: Kevin's disease is a genetic condition he has to figure out how to cope with, which is also man vs. self.
So, yes, any good novel has several conflicts running concurrently. The more there are, the more complex the story.
For Max, the "learning disabled" boy who has low self esteem at the beginning of the novel learns that he does, indeed, have value and merit. Through his experiences and adventures with his newfound best friend, Kevin (who has Morquio's Syndrome, and is deep denial of his impending mortality), Max learns to read, and eventually write his experiences, which turn out to be the book, "Freak the Mighty," itself.
For Kevin, our tragic hero, his flaw is his outward denial of his disease, which has left him stunted in growth, though his mind is far beyond those of his 7th-8th grade peers. He has strong transhumanist views, ultimately wishing to be surgically given a "new body." His fascination with knights and robots brings us a theme of human frailty and its need for mechanical improvement, which is ultimately ironic, considering Max's newly gained "strength" of mind and selfhood, the opposite of physical weakness.
Another theme of the book is that one does not have to turn out like one's parents, as evidenced by Max using his great size and physical might in only beneficial ways (despite some tantrums). He proves this to the community after he escapes his father. Max did have something to prove, and this frightening experience teaches us that we do have some control over our destiny. Another irony: Kevin did not. Hence his flight into his transhumanist delusion.