Absolutely! Collect cubes from any city you pass through or end in, just not the city you started in (in the case of someone depositing their cube there after you were already in the city).
Let's say I move 2 spots - first to an orange city then to a green city - and pick up intel cubes in each. But the first city I pass through completes a pair (then I continue on to the green city).
Do I get the intel card for the green or orange region? We played it as you get the orange intel card because the cube that completed the pair came from this region - even if we didn't actually stop there...