Why did one pecan pie end up with a dark center after baking while the other pie came out perfect, same batter same cook time?
As Ron Beyer alluded to in a comment, two pans on different oven racks can end up cooking very differently.

Remember, the heat comes from particular parts of the oven: for an electric oven generally top and bottom heading elements, and for a gas oven convection from the bottom. 

Pans placed close to the bottom of the oven will get extra coming on the bottom and middle of the pan, due to the radiant heat. Pans placed close to the top of an electric oven will likewise get radiant heat from the top. If you have two pans on an electric oven, the top one will additionally shuttle the bottom one from radiant browning on the top.

When cooking on two racks simultaneously, it's a good idea to switch the pans during the cooking process.