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