What are some of Napoleon’s difficulties in dealing with the humans for supplies in Animal Farm?

Other animals object to trading with humans, the humans won't given them a fair price, and the animals are given counterfeit money.

The animals have a rule at first that there will be no trade with humans.  Old Major is very specific about this when he lays out his philosophy of Animalism.  The animals are to avoid imitating humans or having contact with them.

No animal must ever live in a house, or sleep in a bed, or wear clothes, or drink alcohol, or smoke tobacco, or touch money, or engage in trade. All the habits of Man are evil. (Ch. 1) 

This doesn’t last long though.  Soon, the pigs become more and more like humans.  Eventually, they live in the house, sleep in the beds, and drink alcohol.  The prohibition against trade is also lifted, because Napoleon cares nothing about the tenets of Animalism, and is more interested in his own power and comfort. 

From now onwards Animal Farm would engage in trade with the neighbouring farms: not, of course, for any commercial purpose, but simply in order to obtain certain materials which were urgently necessary. (Ch. 6) 

The animals are confused about this, but Squealer assures them that the resolution against trade was never real.  It was “pure imagination.”  The animals need to trade with humans in order to get supplies for the windmill.  Mr. Whymper, “a sly−looking little man” is their go-between.  They will trade with either Frederick or Pilkington, but never both at the same time. 

Things go awry when the animals sell a pile of timber to Frederick, and he cheats them.  The whole process is a mess.  First it will go to one farmer, then the other, and the animals can't get a good price.  They use propaganda to turn the animals against one farmer, then the other.  There is excitement when they are finally paid, but it turns out that they were paid with counterfeit money. 

Whymper, his face deadly pale, came racing up the path on his bicycle …. The next moment a choking roar of rage sounded from Napoleon's apartments. The news of what had happened sped round the farm like wildfire. The banknotes were forgeries! Frederick had got the timber for nothing! (Ch. 8) 

The farm is short of money, and the pigs arrange for more of the hens’ eggs to be sold.  There was a mutiny for a while at the first suggestion of this, but eventually the hens relented.  Now, everything is rationed but the pigs do not seem to be suffering.  They are even putting on weight!