You mentioned the old problem of Sectoids not showing up after a certain point. This isn't an issue in Enemy Within. Normal Sectoids continue to show up throughout the game (in smaller numbers) as part of Mechtoid and Sectoid Commander groups.
Meld canisters start counting down immediately, whether you see them or not. Also, the "Meld this way" indicator that happens at the start of some turns does not grab the camera, so if you hear the Meld sound, cycle through your soldiers quickly to find it. You missed 2 on this map b/c you were fiddling with some other soldier's move options.