"We were already trailing in the fifth minute."
Translation:V páté minutě už jsme prohrávali.
How come in this sentence the "jsme" in not in the second position? What am I missing here?
First, it is not a hard rule, it has quite a few exceptions.
Typically you can switch "už jsme"/"jsme už", at least unless a declarative sentence starts with "Už jsme...". That is because "už" is also short and does not move "jsme" to a stressed position when it switches its place with it.
Then, "v páté minutě" is a separate unit in the sentence, the second position comes only after this unit.