How so? Were the Crusades not fought under the banner of the christian church? instigated by the popes?
The very first paragraph in Wikipedia's entry for each states: 
1) 'The Crusades were a series of religious wars sanctioned by the Latin Church in the medieval period. The most commonly known are the campaigns in the Eastern Mediterranean aimed at recovering the Holy Land from Islamic rule but the term Crusades is also applied to other church-sanctioned campaigns.'
2) 'The Inquisition was a group of institutions within the government system of the Catholic Church whose aim was to combat heresy.'

Feel free to explain, however, why these church-sanctioned events should not be considered cases of  'christians behaving very badly'.