Unfortunately in the rulebook the example picture used to discuss placing a pheremone is focused on mushrooms. It shows a long 3 tile piece where it's being placed with the middle part over the mushroom. Turns out that middle part also has the 2pt scoring symbol as well. This is confusing as it (inadvertently) leads one to think you don't get cubes where there are pts markers.
Livin's mostly wasting time, and I waste my share of mine
I am a breathing time machine
I can see how this might be confusing, but you get the points when placing the tile. The position of the cubes isn't really relevant after you've determined what to place based on the hexes you cover up.