“PAA – What you said about someone being killed isn’t true – they saved Buckbeak, remember? I guess it’s just something we can’t understand…”
That just means that Buckbeak hadn’t actually died the first time around. If you read the passage carefully you’ll see that it doesn’t ever say that he died; all it says is that they heard the axe. But they didn’t actually see what happened. When they go back in time we find out that what they heard was Macnair hitting the ground in frustration.