For this gem, go up to the second floor of the shops, on the right side and move Luigi towards you, up to the gate that separates him from the plants. At the end, there is enough space to do a ZR+ZL and free up an access. Take this new passage that will take you over the entrance, then search in the chest to get the white gem.
Head to the first shop on the first floor, the first after passing through the swing door: throw a suction cup on the dummy on the far left and pull on it to open a hatch leading to a chest containing the red gem.
On the second floor of the shops, go to the far right, just next to the guard's room. Flash the vending machine 3 times so that the blue gem comes out.
On the second floor of the shops, on the far left, you can see a metal plate on the floor: use the Dark-Light Device to reveal a new ladder. Go up there and then go right and open the chest containing the gem, but beware, it's full of bats!
In the upstairs toilets, first on the right after the elevator, use the Dark-Light Device to reveal a grate. Take Gooigi inside, and cut off the water that was blocking his passage until then. Go back to Luigi, remove the aeration and take the gem with Gooigi.
The yellow gem is in the window in the shop on the top left,. Hold one of the sturdy suitcases and swing it on the glass so that it breaks and releases the gem.