Bukhari and other compilers of the traditions ascribed to the Holy Prophet set different measures for the acceptance of a report. Though conditions set by Bukhari are the strictest, as you have stated, and his book is considered very authentic but Muslim scholars do not, generally, hold that a tradition recorded in Bukhari (Or any other book containing Sahih traditions) is fault-free and should necessarily be considered as the exact actual saying and/or action of the Prophet (sws). As we all well know that even Imam Muslim, a disciple of Bukhari didn't take the principles set by his teacher and established his own principles and compiled a different book. Other Muslim scholars also did the same and compiled books of their own. This testifies to the fact that Muslim scholars never took the Sahih of Bukhari as the final and ultimate source for the absolutely true reports about the Prophet (sws).
As regards the question of contradictory reports, no human endeavor is free of error. What Bukhari and Muslim and other compilers of the traditions of the Prophet did is to apply strict checks on acceptance of a report about the acts and sayings of the Prophet (sws). They honestly established checks and then compiled the traditions accordingly. They presented what they understood to be authentic. Now it is possible that to them the reports, which we find to be contradictory, could be reconciled. Or, on the other hand, they may merely had mentioned them finding them to be equally authentic from the perspective of the chain of narrators, because they didn't want to reject a saying ascribed to the Prophet (sws) as they may not have been sure of which of the two or more contradictory was actually the true one. Nevertheless, the presence of such contradictory reports or reports bearing any flaw doesn't deprecate the academic work done by the great scholars. However, to hold that their works are error-free is to give their work a position, which no human effort can deserve.