I went back and read the Bible again, this time going contra-spotting. I have come up with a few, which I will list here.

First, and foremost to me( and I would think to theists as well) is the question: Is God good to everyone, or a few people?

PSA 145:9 The LORD is good to all: and his tender mercies are over all his works.

Vs.

JER 13:14 And I will dash them one against another, even the fathers and the sons together, saith the LORD: I will not pity, nor spare, nor have mercy, but destroy them.

Secondly, is God a bringer of peace, or a warlord?

EXO 15:3 The LORD is a man of war: the LORD is his name.

Vs.

ROM 15:33 Now the God of peace be with you all. Amen.

And, for me, the most glaring contradiction of all: Which order did god create the world in?

Did he:

GEN 1:25 And God made the beast of the earth after his kind, and cattle after their kind, and every thing that creepeth upon the earth after his kind: and God saw that it was good.

GEN 1:26 And God said, Let us make man in our image, after our likeness: and let them have dominion over the fish of the sea, and over the fowl of the air, and over the cattle, and over all the earth, and over every creeping thing that creepeth upon the earth.

Or did he do it in this order?:

GEN 2:18 And the LORD God said, It is not good that the man should be alone; I will make him an help meet for him.

GEN 2:19 And out of the ground the LORD God formed every beast of the field, and every fowl of the air; and brought them unto Adam to see what he would call them: and whatsoever Adam called every living creature, that was the name thereof.

Just a few to start off. Fellow atheists, feel free to give your 2 cents. Theists, feel free to try your hand at clarifying this.