Bacteria contamination inside a thermos bottle
The assumption that it was sterile is wrong. Standard cooking leads to a reduction of bacteria to about log6, so 1 in 100 000 survives. Afterwards, these bacteria multiply exponentially in your soup, potentially achieving levels at which people can get sick. 

Your logic will apply to canning. But it is known that the "fill the cooked food into an airtight closing container" is an unsafe canning method even for high acid foods, and a thermos bottle is not guaranteed to be closed airtight. If you want to can soup, you have to follow safe canning procedures, which include a restriction of the ingredients you can use, a restriction in the liquid/solid ratio, the prescription of proper containers, and a sufficiently long sterilization step in a pressure canner.