This appears to have happened at least a couple of times over the course of the conquest of Chinchaysuyu, the northwestern part of the Inka empire. The story goes that the Inka emperor Pachacuti dispatches an expedition, led by a general named Capac Yupanqui to the coast. Capac Yupanqui returns without establishing territorial control, and Pachacuti sends him out again with orders to conquer up to a certain river valley (the Yanamayo) but no further.

At some point during the campaign, a group of Chancas (a small conquered ethnic group within the Inka army) rebel and attempt to flee. Capac Yupanqui gives chase and follows the to the highland town of Cajamarca. There, the Chancas ally with the coastal Chimú state, one of the last real rivals the Inka have yet to conquer. Somehow, Capac Yupanqui is able to defeat this coalition and establish Inka dominance over several of the small highland Kingdoms surrounding Cajamarca. The Chronicles disagree about whether the Chimú are defeated and totally conquered or whether they suffer a military defeat but are still independent by this point. Capac Yupanqui then returns to Cuzco expecting to be celebrated as a military hero, and is promptly executed by Pachacuti for crossing the river against orders.

At this point, Pachacuti names his son Topa Inka Yupanqui commander in chief and sends him north to conquer the areas that Capac Yupanqui didn't. In the course of his conquest, he expands Inka territory into modern Ecuador. He also supposedly goes on a voyage to several Pacific islands, possibly the Galapagos. On his way back south, Topa Inka Yupanqui conclusively conquers the Chimú and takes a large amount of their gold and silver back to Cuzco. When he gets back with his army, Pachacuti once again doesn't seem to have been entirely pleased. His son and heir had returned a conqueror, but he had been gone for six years. In his annoyance, Pachacuti order the execution of two generals (also his sons and Topa Inka Yupanqui's brothers).

It seems that in both cases Pachacuti was removing any chance that someone would contest his chosen son and heir's claim to the throne.

edit: cleared a little bit of wording up

Secondary source:

Rowe, J. (1945). Absolute Chronology in the Andean Area. American Antiquity, 10(3), 265-284. doi:10.2307/275130

Primary source:

Gamboa, Pedro Sarmiento de

1532 The History of the Incas. Translated by Brian S Bauer, and Vania Smith. University of Texas Press, Austin. page 134 for Capac Yupanqui story. Chapter 46 for the execution of Topa Inka's brothers (can't remember the page number now).

Here's a digital link: http://www.galapagos.to/TEXTS/SARMIENTO.HTM