It's all in the CG software. Before that, they would tie the limb back at the elbow or knee and shoot in such a way as to disguise it. Today, piece of cake for the post-production geeks.
The film's director, Ana Lily Amirpour, wrote an article devoted to this topic which is posted at the Alterian website (Alterian is the effects company that made the amputee shots a reality), It's titled, "How They Did It: Designing the Amputee Protagonist of Ana Lily Amirpour's Dystopian Desert Trip, The Bad Batch". The shots were, as the previous answer notes, a mix of CGI and practical effects, though there was more practical-effects trickery involved than you might think. Alterian created a prosthetic "stump", from the shoulder down, for Suki Waterhouse to wear, while her real arm was painted green and held somewhere in front of or behind the prosthetic (depending on the angle of the shot). CGI deletion of her real arm from each frame completed the shots. For the missing leg, they relied even more on purely-practical effects: Waterhouse's real leg would be hidden from the shot by burying it in the sand, sticking it through a hole in a mattress, etc.
