The total momentum of the two lumps, both before and after the collision, is zero. Momentum is conserved. KE was positive before the collision, but was zero afterward. Careful measurements would show that the lumps are warmer afterward; the initial KE changed into thermal energy. The difference arises because energy, unlike momentum, comes in many forms and can transform into other forms. If one keeps track of only one form of the system's energy, it will rarely be conserved.