When you clone build, you get a huge up-front cost equal to the amount of money displayed when you clone. I believe this is the cost of walls and foundations, not items. However you then get charged again for the actual materials (i.e. a ton of bricks). This actually bankrupted my prison because I cloned a big section of cells and suddenly went into the red unexpectedly.
I'm not sure if this affects foundations, but it definitely appears to not affect items (they don't add to the displayed cost). Either way, an extra $10,000 charge early in a prison's life can be deadly. If you fill out the walls then clone build, it seems to avoid the issue.
