Conjoint analysis uses specialized data collection methodology while factorial analysis does not.  A conjoint analysis survey uses trade-off heuristic that is thought to be representative of how consumers choose between alternatives (Price, Features).  It can also help reduce response burden because not every respondent needs to be given every choice/combination.  In contrast, a survey that will be using factor analysis the respondent would judge every feature and combination of features.  These two methods of analysis are very different  in how data is collected.