Any christian holy war that can be considered one, e.g. the Reconquista, the Baltic Crusades, and the campaigns in the Middle East against the Egyptians. Are there any records of groups of peasantry/soldiery/nobility that disagreed with the notion of crusading/using violence to enforce religion on those that they deemed as infidels and heretics in these wars?
There were complaints on the actions of specific knights suggested by William of Tyre. He complains that the actions of the Templars in the battle of ascalon in 1153 were motivated by "lust and greed." Something that Saint Bernard had spoken against in his "In Praise of New Knighthood" That knights were not supposed to be motivated by these things if they are within god's will.
I think it's important to remember that the critiques were coming when the actions were not inline with what was considered correct actions within holy war.
There were also instances of people who supported the movement not supporting specific crusades. For example, Abbot Suger in Saint Denis France, did not support the second crusade. This was probably due to his disagreement with Saint Bernard on the decorations within monastic churches.