Sophie is a Polish Catholic, not a Jew, so it's a perfectly valid question to ask why she's sent to Auschwitz. Indeed, Sophie, herself, doesn't really understand what she's doing there. She keeps saying to herself "I don't belong here." But the Nazis don't make such a distinction between Sophie and the predominantly Jewish population of the camp. As far as they're concerned, all the inmates of Auschwitz are subhuman, so Sophie's loud protestations of racial purity are of no avail.
Sophie appears to have been caught up in a sweep carried out by the Nazis against the Home Army, the Polish resistance movement. Although Sophie didn't lift a finger to help the resistance, she nonetheless shared a common dwelling place with Wanda, who definitely was involved in subversive activities. Guilt by association was often sufficient reason for the Nazis to send people to the camps, and this would appear to be the best explanation for Sophie's terrible fate.