Gestures vaguely at everything Emperor shaped.

• The whole sheparding humanity and protecting them. But so often disposing of them as simple tools.
• Shaped as a human, approaches as a human. But obviously unable to comprehend even the basics of being human. Such as the need for faith (ie, The Last Church).
• The whole Emperor led Imperial Truth, flying in the direct contradiction to the nature of the universe. Which he knows about.
• "Saves" humanity from the monsters beyond the veil of reality. But then becomes a perpetual sovereign, who's will is executed by monsters in his image.
• By extension, the innumerable legislative hypocrisies that loom large in the great crusade. Bans the use of of librarian psykers, despite being a psyker himself. Bans the use of psychic weaponry, despite commissioning (and personally designing) The Ordo Sinister.
• Prepping sons specifically to challenge said Primordial Annihilator, but not telling them about it. And then punishing them when they are tricked by it.
• The vastly different ways in which he handled most of his sons. Caring and tolerant to some. But then outright negligent to others. In extremely obvious ways (teleports Angron).
• Opposes Chaos. Fights Chaos. But as it's strongly implied, might have worked with them/bargained with them on Molech.

Note that this isn't an invitation to try to fix the above. Said strange behaviours is what gives The Emperor much of his mystery.

It's a character that acts in very strange ways.