There's many such examples though I'd highlight one in particular as to why the Warrior of Light and the Scions are morally grey at best. Namely that time when they decided to go and brutally murder a pregnant woman in Norvrandt who just so happened to be in the way as a consequence of being displaced by the actions of the protagonists themselves.

Reasons can be brought up as to why it was a grim necessity though I daresay when people have to start defending the death of pregnant women then it should not really be much of a surprise if others doubt the supposed 'overwhelming goodness' of the game's protagonists.

Of course, I suppose it helps that the pregnant woman in question was an off shoot of the Sahagin! I imagine the situation would be taken very differently by most if it was a pregnant woman who looked like Venat, Lyse or Y'shtola instead.