I'm sorry about your little turtle.
See
http://www.fishpondinfo.com/turtles/turhealth.htm#shell under deformed shells. I just put up two photos of a red-eared slider with a deformed shell. Such problems can be genetic (born that way) but often are a result of one of the following: improper diet deficient in something, improper full spectrum lighting, cramped quarters, etc.
Did the baby have a strange shell shape when you got him? With proper diet, lighting, and setup, the baby may improve with time but probably will never be completely normal. If he/she has trouble swimming, then the shallow water was a good idea. Otherwise, be sure he/she gets enough to eat (the other one may get to the foods first), lots of variety in the diet, good lighting, etc.
My page on baby turtles is at
http://www.fishpondinfo.com/turtles/hatchling.htmI suggest taking the turtles to a vet for a consultation and advise as well.
Good luck!