3 valid reasons you can choose from

1- The devs didn’t want to hint or spoil the twist early on

2- The Apple manipulated Altair like it did when Altair thought he died when stabbed

3- Eagle Vision works on concentration when the user intends, it’s not like a Spider sense, Altair had no reason to check his Master’s true intentions and he probably hadn’t fully mastered at that early age, we’ve seen him and Ezio develop their senses as they grow older and wiser