Don't know the detail, but there's a suggestion in several of the articles reporting this that Network Rail will fail to deliver the infrastructure improvements that Virgin/Stagecoach was told would be in place.
Therein lies one of the key problems of the privatisation model - Network Rail is supposed to be delivering improvements across the entire network; operators bid on the basis of these improvements being made to schedule; then Network Rail (seemingly invariably) fail to deliver on time, thereby giving the operator the opportunity (sometimes justified, sometimes not) to say we can't deliver what we promised because the infrastructure doesn't allow it, so you (Network Rail/Government) need to bail us out/compensate us/let us off our commitments.
Network Rail is owned by the government and, to put it mildly, does not have a good track record when it comes to infrastructure delivery.