Object with many children will not show up in the center although its coordinates are set to 0, 0, 0

I am doing a Rubik cube generator. Each of the pieces are basically a 1x1 cube which will be repeated in the shape of a bigger cube in my code as children of an empty object. The empty object is in the exact middle of the pieces, and all the pieces have their origins in the exact middle. However, when I put the empty to the center of the scene (0, 0, 0) It shows up in a different place.
Here are some pictures from the editor:
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^As you can see, the empty is in the center with coordinates set to 0, 0, 0
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^Now ,when it has children and the coordinates are all still 0, it shows in there

Based on your information we can not really tell what is wrong. Where do those cubes actually come from?

Some time ago I’ve already answered a Rubik’s Cube question and I’ve written this 300 lines script (which I’ve linked in the answerer over there) which does create a Rubik’s Cube out of 27 default cubes. It actually creates a custom mesh on the fly based on the default cube mesh and uses vertex colors to color each side as expected.

We’re happy to help you out with your specific issue, however there are no images in your question and based on your description it’s impossible to tell what might be wrong.