Also, lands like Patagonia and Chaco were settled (by Europeans) very late in Argentina's history, for example. For a long time, Peru and Mexico were the greatest population centers in Spanish America, due to intermarriage with the already large native population.
Let's just say that, in Argentina's case, the Spanish liked to go and found new cities with pompous names wherever they could plant their flag, and just hope they would survive. For example, the first founding of Buenos Aires fell to Indian raids and starvation. Many other early cities in Argentina were destroyed by Indians tired of the mistreating brought by the Spanish. Most colonists came from Peru or Paraguay, where populations and power structures were well stablished, and the rest came from Spain itself as a trickle. For the most part, the early population of Argentina were mestizos from the native populations, sometimes by Spaniards taking native wives, other times by Jesuitic missions who built pretty sophisticated settlements.
And the sailing and mapping wasn't what we could call... efficient... There are many bays and geographic points called Puerto del Hambre, for example in Patagonia (I'll leave the translation to you...), and for a long time, Tierra del Fuego was tought to be part of a larger Terra Australis that did not exist. Many early maps of South America are deformed too.