The lilliputians have been growing magic cucumbers that, when eaten, temporarily lets them grow to the size of a normal person. They've all gotten addicted to their newfound gigantism, but either the crop cultivation or their greater-than-normal size is having negative side effects on their environment that aren't easily noticed until viewed from a great height.
The large size of these tiny people has several unintended environmental effects I can think of. Here are a few possibilities:
Consumption: When large, the Lilliputians eat for a larger being. They consume large amounts of plants (and possibly animals) and are devastating the local area. They only eat the materials away from their villages, sparing their crops, so the impact isn't immediately apparent to their small versions. The more they eat, the longer they stay large. And they really like to stay large...
Large Environmental footprint: In this case, literally. Huge footprints are crushing vegetation, generating puddles and eroding the banks of local rivers. Mud from giant footfalls is choking the streams and the foot falls are crushing the burrows of mice, insects, and worms. Until you look at the effects spread across the landscape, it's not obvious.
Giant Lilliputian Goats: The teeny tiny goats these people keep get into the cucumbers and become enormous. It's an excuse for someone to become gigantic and drive them away from the villages until the sheep shrink again. But if the Lilliputians have a big appetite when enlarged, the goats have it in spades. The goats can eat almost anything, and do so. Since the goats keep eating constantly, and the longer they eat, the longer they stay large, they are causing large swaths of land in the region to be mowed down to nothing.
Giant gigantism: While the Lilliputians eating magic cukes become big, the "normal" sized animals become truly titanic - and equally hungry. Since the area immediately around the Lilliputians is already starting to thin out in vegetation, these titans are moving further afield in search of food, REALLY devastating the landscape. Think of dog-sized grasshoppers gnawing away perpetually at everything in their path, staying big constantly by eating everything...
Constructive destruction: The Lilliputians in giant form have been digging canals, draining swamps, leveling hills, and doing all the things humans would do if suddenly given titanic power. But they have no experience with the consequences, and their fields are watered at the expense of streams drying up, and runoff flooding streams. Mining efforts have left vast areas ripped up from searching for (fill in valuable mineral here). It's always in the next valley, or downstream, and out of sight is out of mind.
Oversized impact on soil: The cucumbers make small cukes, but take nutrients out of the soil like large plants. While they keep rotating the fields they grow the cucumbers in, observation from on high reveals that all the fallow fields left to recover aren't. Only the scraggliest plants are growing there, and the soil is taking far longer to be restored. If they aren't careful, all their agricultural land will be useless for years before it can support crops agin.