Because it's poor accounting. Given the scale of the US military and it's annual expenditure just existing, to make a fair comparison you should at least take account of the marginal cost of the war, not the total cost.
There is also the opportunity cost to take account of, but that's much harder (impossible?) to put an accurate figure on.
It is, of course. Nobody is calculating the cost of the war as the defense budget multiplied by the time. The cost includes about $750 billion in direct appropriations for the war itself (separate from the overall defense budget), plus numerous indirect costs such as additional medical care and disability payments to veterans, replacement of destroyed equipment, and interest payments due to increasing the national debt.
There is also the opportunity cost to take account of, but that's much harder (impossible?) to put an accurate figure on.