Because on page 5 of volume one where he is explaining the various contents of the Qur'an, he says some parts of it are abrogated and others are abrogating, some parts are explicit and others are vague, some parts of it are general and others are specific... then he says:
ومنه على خلاف ما انزل الله
"And some parts of it oppose what Allah has revealed."
Then he even gives further examples as to what he means on page 10, he says:
واما ما هو كان على خلاف ما انزل الله فهو قوله " كنتم خير امة اخرجت للناس تأمرون بالمعروف وتنهون عن المنكر وتؤمنون بالله " فقال ابوعبدالله عليه السلام لقاري هذه الآية " خير امة " يقتلون امير المؤمنين والحسن والحسين بن علي عليه السلام؟ فقيل له وكيف نزلت يابن رسول الله؟ فقال انما نزلت " كنتم خير ائمة اخرجت للناس
[As for what opposes what Allah revealed, then it is like his saying {You were the best nation brought forth for mankind, you enjoin what is good and forbid what is evil and believe in Allah} Abu `Abdillah (as) said to the one who recited this verse: "Best nation!?" They killed `Ali and Hasan and Husayn (as)!? They said: "Then how was it revealed O son of Rasul-Allah (saw)?" He said: It was revealed as {You were the best Imams brought forth for mankind}]
And he gives other examples of verses he believes were corrupted by the companions to hide the virtues of the Imams.
Is this not clear?