FAQ

It's not made clear in the story but a likely explanation is that they're armed soldiers fighting for some cause of independence in the territory against the national government, whatever that may be. They probably wander between settlements seeking food and shelter and with their assault rifles, they probably intimidate the locals into giving them what they want.

They may have been hiding from Allie and his party because they were suspicious of them: they could have thought that Allie was a government official sent to find them or any of their comrades in the region. Allie talked to them and told them to drop by Jeronimo if they could, which led to bigger problems for Allie.

The farmer was looking for a way to refrigerate his crops, which were rotting in his barn. It would seem the farmer was unable to move his produce very quickly, perhaps because of a failure in the market. If anything, Allie probably should have tried to convince the farmer that his invention could be used to move chilled air like he did when he built the full-sized version in the jungle and hooked up a series of ducts that provided his family's home with cooled air. However, Allie couldn't get beyond the farmer's rejection of the machine and decided to leave.

Allie, not wanting the men to resort to threats or even violence in refusing to leave, thought that the imagined infestation would be enough to drive the men away. At first it seems the men knew he was bluffing or simply didn't care so Allie set about destroying much of what they'd built trying to convince them the infestation was real. It didn't work and only compounded the problem when the men still refused to leave.

The men had obviously spent a lot of time, perhaps their entire lives, living in the jungle and were hardy enough to survive there, so the threat of an insect infestation wasn't a very convincing argument on Allie's part. The men knew they had access to a great spot to continue whatever mission they were conducting and also could threaten Allie and his village with violent reprisal if they were defied.