I have an animation, and some of the frames are lining up incorrectly. Is there a way to manually reposition them?
Did you try offsetting the image’s points?
It works if I change the values, but oddly only if I alter the origin values.
But it worked, so thank you. 
I think the centre value is for things like rotation, but i might be wrong. You’re welcome 
No, you’re totally right, the Origin is used to positioning a sprite: When you set a sprite position to X;Y it means the object will be placed so the Origin is at X;Y (in the non rotated sprite, then it’s rotated I think).
And the Centre point is the point the sprite is rotated around (not sure if this sentence makes sense in English 
)
I like to change origin point to the bottom center of a platformer character for obvious reason.
Also I think the engine has some bugs if you change center point to a value that is not in the middle. Sometimes the center point from previous animation is used when you change the animation.