£40,000 is a tiny drop in the ocean of money that the MoD spends each year
It is a drop in the ocean in the amount of public money that government departments and in particular the MoD waste each year. If I can find the figures I will link to them, but essentially the MoD and other departments have been criticised for the amounts they pay for the the most basic of items such as light bulbs and toilet paper and will come up with illogical reasons as to why this happens.
I thought the days of blaming computers instead of or mistakes by humans was long behind us but as you rightly point out "servers do not dial the speaking clock unless told to do do."
But as I have said on more than one occasion until governments give real power to those whose job it is to oversee spending of public money then these types of stories will continue to surface.