If there are some discrepancies in a few narrations in Bukhari Sharif then how do people define some narration to be manipulated and if some are manipulated then what about credibility of all others considered as authentic? Does this mean a student of Hadith has to be skeptical at start while reading Bukhari?
Imam al-Bukhari himself indicated that his collection was not 100% Sahih as per the way he would transmit the narration, and there are several.
Imams like ad-Daraqutni, al-Aqili, ibn Hazem and even Ibn Hajr confirmed there are weak hadiths in al-Bukharis Jami.
The problem is, Hadith science is a man-made science and it can be changed at anytime. Some scholars were strict while others were lenient. So the authenticity of a hadith scums to the character of a person and it has nothing to do with the reality, because it's quite impossible to know if a hadith is truly from the Prophet.
EDIT: Here is an example of how a hadith can be authentic to one person and unreliable/rejected by another...
Lets look at a person named Ibn Shihab az-Zuhri, a student of some of the Sahaba.
Al-Bukhari, and other scholars, regarded him as an authority in hadith. If a hadith is reported by him they would accept him as a reliable reporter. Many hadiths come through az-Zuhri that al-Bukhari reports in his 'Sahih'. Keep in mind al-Bukhari did not meet az-Zuhri; he relied on other people's views regarding az-Zuhri to consider him as an authority.
Now, there were scholars who rejected az-Zuhri as reliable. He may be an authority, but it does not make him upright and trustworthy. One major scholar who did not consider az-Zuhri as reliable was Layth b. Sa'd. Layth was upright and reliable (thiqa thabt) and people trusted him.
Layth actually met az-Zuhri and they use to have discussions. Layth considered az-Zuhri as a contradictory and forgetful person. So he would not take az-Zuhri's narrations and considered him as abandoned.
Therefore, we have two Imams who had different opinions about az-Zuhri. One who met him and one who did not.
The aftermath of this can be easily seen. Narrations coming through az-Zuhri would be accepted by al-Bukhari, but rejected by Layth b. Sa'd. One would call a hadith 'Sahih' and the other 'Da'ef' or 'weak' if we took az-Zuhri's account. That's a major problem is it not?
And Layth b. Sa'd was not Shia, if anyone tries to label him...
The total weak/fabricated hadiths in al-Bukharis collection comes to 52.
A recent scholar, Imam ibn Amin has written a well detailed book on the weak hadiths in Bukhari and Muslim. You can find it on the internet.
Not all 'Sunni-Muslims' believe Bukhari is 100% authentic
It is IJMA of ummah that all MUTTASIL ahadees in sahi bukhari are sahih, an there is no zauf in them.
I know there are some people now a days who try to convince that 2/3 ahadees are zaeef (weak) in it, but according to asool al hadith they are wrong, you can verify their claim your self and try to be skeptical reading whole bukhari. And if you get convinced about 1 hadees in it being zaeef. Let us know of the reasons.
Note: This conclusion [that Bukhari is 100% Sahih] excludes the chainless, broken-chained reports, or unattributed reports sometimes used by al-Bukhari in his chapter-titles or appended to certain narrations.