Two things that cannot both hold. A conflict is a fact about incompatibility, not about ill will.
Latin conflictus, past participle of confligere (to strike together, clash), from com- (together) + fligere (to strike); two things that cannot both stand, named for the collision rather than for any intent behind it.
Latin fligere is to strike, and the root records a collision, not a motive — two things clash because they cannot occupy the same place, whatever either one intends. Naming something a conflict says nothing yet about who is at fault.