It's hard to say exactly what the problem is from your vague description, but it seems you messed up something in the dimension layer. Start with only one copy of the board and verify it is correct. Then you can replicate that board after you know it's OK.
However, trying to panelize a board yourself is a bad idea in the first place. The board house is much better suited to do this, does this routinely, and has all the right tools for it. Send them a single copy of your board and tell them how many boards you want. They know the size of their panels, and for prototype services can rearrange your copies with that of others to fill up a panel.
Basically, this is a production detail that you as the electrical engineer shouldn't be in. Let the production people do the production in whatever way is most efficient for them. They tell you the price for different quantities of boards, and you tell them how many you want.