The argument is specifically about prehistoric human ancestors and sophisticated tools. The fact that other animals that don't stand upright can make "basic" tools doesn't tell us anything about whether human ancestors needed to stand upright before making advanced tools.

This is strong evidence against the scientist's conclusion. The scientist argues that standing upright must have come before sophisticated tools. But (B) tells us that advanced hunting weapons, which we can reasonably interpret as a kind of sophisticated tool, have been found among prehistoric human ancestors who did not stand upright. If that's true, then those ancestors had sophisticated tools before standing upright, which strongly suggests our ancestors didn't need to stand upright to make those tools.

The fact that many upright ancestors had no sophisticated tools doesn't weaken the argument. The scientist claims standing upright came before sophisticated tools, not that standing upright immediately or necessarily led to sophisticated tools. It's perfectly consistent with the scientist's argument that ancestors stood upright for a long time before eventually developing sophisticated tools.

This is tempting because it seems to undermine the connection between standing upright and the ability to make tools. If those who stood upright had no more dexterity than those who didn't, maybe standing upright didn't actually help with toolmaking. But notice that the scientist's argument is about free use of the hands, not dexterity. These are different concepts. You could have the same level of dexterity in your fingers but still lack free use of your hands if you need them to support your body while moving on all fours. Standing upright frees your hands from the task of locomotion, which is independent of how dextrous your fingers are.

(E) is about whether the users of sophisticated tools needed to stand upright. The scientist's argument, however, is about making sophisticated tools, not using them. The scientist claims that advanced toolmaking requires free use of the hands. Even if using a tool doesn't require standing upright, that wouldn't address whether developing that tool in the first place did.