The main way targets should/would be selected is by direct intelligence. E.g. the targets should be identified through satellite or other observations. It's hard to imagine that a building that has operated for some length of time as a school would not have patterns that are visible from satellite vs. military facilities with different patterns. You also don't just randomly attack structures in this sort of surprise attack, you're presumably aiming for some specific people or equipment with some priority/military goal in mind, so you really want to have observed the targets and patterns and have up to date information on their usage.
I think what likely happened here is that the entire base was the "unit" of targeting and the mistake was in identifying which buildings were part of the base. In the satellite view the military buildings and the school look very similar (since the building as I understand it used to be part of the base but was repurposed as a school).
It's not true that whoever made the error had all the time in the world. Presumably once the order was given there was time pressure given that the strike was to be timed with the other intelligence.
In theory the US military should/is supposed to have good processes around this stuff. So we are told. Obviously failed in this case. It is a tragedy.