I'm not seeing the modified properties of the layer in your comp. When ever I run into something unexpected I select the layer and press the U key twice to show me all of the things that are not in their default position. I noticed that you have a custom frame size set for the comp. I'm assuming that you set the composition background color to gray or there's a layer that we can't see. You do know that the Comp background color will not render right? There is no reason to change the comp BG color from the default black unless you are doing some kind of pre-multiplied with alpha export that is not part of an ordinary workflow.
Are you new to AE? Is this a new problem?
What happens if you re-launch AE, reset your workspace, create a new comp and then double click something like the Ellipse tool to create a new shape centered in the comp space?
If you can't solve the problem and AE is up to date then we need OS and AE details down to the last decimal point. By up to date I mean latest build of the version you are using, not latest version.
I reset the workspace and it worked! Thank you for the help. I don't know why I didn't think of that before.
And I changed the default background color to grey in another project because I was having issues discerning the transparent background from my assets.