Does Istigfar (Asking Allah for forgiveness) between the first and the second part of Friday prayer`s sermon render the prayer invalid?

Talking during Friday prayer`s sermon is disliked, but there is no harm in offering Istigfar between the two parts of the sermon, and it doesn`t invalidate the prayer as it is actually from Sunnah. And Allah Knows Best.

Does the deceased hear the supplications or recitations of those visiting his/her grave? And does making constant supplications for the deceased who didn`t adhere to performing the prescribed prayers ameliorate his/her affliction?

Praise be to Allah the Lord of the Worlds.

In principle, the dead hear the living since it has been rigorously authenticated that the Prophet (PBUH) ordered the bodies of the idolaters slain in the Battle of Badr to be buried. He then approached them and called them one by one and said: "Have you found what your Lord promised to be true for we have found what our Lord promised us to be true." Umar asked him: "O messenger of God! Why do you speak to lifeless bodies?" The Prophet (PBUH) replied: "By the One Who has sent me with the truth! You do not hear my words better than they do except that they cannot respond." [Agreed upon].

However, not all the deceased are in the same situation because Allah The Almighty Knows: "Before them is a Partition till the Day they are raised up." [Al-Mu`minun/100]. Moreover, supplication reaches the deceased. And Allah Knows Best..

Should one obey his mother even if she was wrong?

Obeying one`s mother is an obligation in matters that are beneficial to her and so long as she didn't drive her children to commit an act of sin.

What should one who made an intention, at night, to make up for a missed fasting day, but broke his fast on the next day?

One who started making up a missed fasting day, then broke his/her fast without a legitimate reason is considered sinful, and is only obliged to make up for the missed fasting days. And Allah Knows Best.