Corrected entry: Gus got upset when he saw that Jim had planted a tree, and there was no indication that the Avalon was designed or equipped to adequately handle live trees, flowers, vines, shrubs, and grass on board, but Jim apparently planted a large roomful of these things. When the first tree was planted, the Avalon would not reach Homestead II for about 90 years. The roving robot vacuums would have had to be removed from this area to enable grass to grow, and there's no explanation for how the plants could be watered (and without causing damage to the floor) or where all the fallen leaves went. Tree roots can push objects in their path, potentially causing structural damage to the Avalon. Avalon may have been very advanced, but failures had occurred without the added "cargo." Without being specifically designed to allow such growth on board, surely problems not anticipated would occur over the decades in space, risking all the passengers... even the ship.
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Correction: This is all based on speculations. They had plenty of time to develop a good ecosystem for the plants before they died, finding a way to manipulate the ship and robots to help watering and keep the area clean. Possibly even direct and cut roots.
lionhead