In the early portion of the movie, the natives are shown harvesting corn (Zea maize), the ears of which are far larger than a human hand. At the time of the Jamestown colony, native corn was typically the size of a human thumb, rarely ever bigger. Large corn, such as pictured in the movie, is a product of seed selection and genetic research, mostly done since the 1860s.
Just prior to the marriage proposal by Rolf to Rebecca, they are seen walking through a large field of foxtail grass. Foxtail is a European/Asian grass, and was introduced to the Americas far later than the colonial period. A field of green foxtail or yellow foxtail could not have been present for them to walk through.
Whilst walking around the ornamental gardens in wonder, the Native American walks along a path with cast iron bollards. Though the movie was set in the 1600s these where probably made during the industrial revolution some 150 years later.
In the scene where Smith and the small party set off up river to find the "king", there are three wooden channel markers visible in the background. The size and shape indicate the markers were not placed there by the Native Americans of the 1600s.
When Pocahontas is approaching with the Native Americans to give food during winter, she is wearing a hide over her head which is of an axis deer. This is native to India and Sri Lanka and would not have been in America in the 1600s.
When Smith first encounters Pocahontas, a nightingale is heard singing in the background. Nightingales are not native birds in America and, unless the settlers brought some with them, should not be heard there.
Smith is shown being ordered to leave Jamestown by the king, but in reality, he had a gunpowder accident, and suffered severe burns. He had to leave for England, and recovered. Pohcahantas was told he died on the trip to England.