Having been curious about Vision and War Machine's absence in the Lagos action scene since Captain America: Civil War was first released back in May, I asked directors Joe and Anthony Russo about it when I recently had the chance to interview them over the phone. Explaining that I was basically in search of a No-Prize answer, I asked why the Avengers weren't fully assembled in that early sequence, and Joe Russo delivered a totally reasonable explanation:

We wanted to show that the Avengers were functioning like a military unit now - that they would take specialist into each location dependent on what was required. They're beginning the mission undercover, and it's easy for Wanda and Natasha to be undercover. They have the eyes in the air in Falcon and Cap, so we wanted to kind of create this idea that they're dealing with hotspot issues all over the world. And Vision and War Machine can be dealing with one problem, while they're off in Lagos dealing with another problem. So they divide and conquer using their resources on a mission dependent basis.

Given that the Avengers mission in Lagos winds up going horribly wrong, with Scarlet Witch accidentally causing massive collateral damage, hindsight suggests that Vision and War Machine probably would have been helpful assets in the field. Then again, they may have simultaneously individually been working on something equally important, so it's hard to fully judge without all of the facts.