We show that nonequilibrium molecular dynamics simulations of elongational flows are inherently unstable over long periods of time. This instability leads to a catastrophic nonequilibrium phase transition that destroy the true structure of the fluid. We identify the source of this instability as a lack of momentum conservation, resulting from numerical round-off errors. We show that this error grows exponentially in the direction of compression, and present two numerical recipes that involve only minor perturbations to the particle trajectories to guarantee momentum conservation.