"Con-" from "concrete" is indeed the same prefix as the "con-" from "continuous" and in both cases it means "together".
However, "-crete" from "concrete" is not the same suffix as the "-crete" from "discrete".
"-crete" from "concrete" means "grown" (it is the participle of the Latin verb "crescere", to grow), so "concrete" means "grown together".
"-crete" from "discrete" means "sifted" (it is the participle of the Latin verb "cernere", to pass through a sieve, to separate), so "discrete" means "sifted away", it comes from the same source as the verb "to discern".