What if the Matrix got a nasty virus?

Each are anticipated. Even a situation where one says "yea but even that can double" has been manipulated with a series of algorithms that are not merely stagnate as in just there to work, these algorithms are what is known as fluid. Fluidity theory is the idea that reality is constantly recreating itself a split second after each exact moment in time goes by. Therefore there is no past only future and the immediate now. Using this theory it is possible for the matrix to be "crashless". This is prevented in two ways. First the fluid algorithms and second the fact that there is no past prohibits the time that anything within the matrix can live.