The exterior of the surveillance shack does not match the interior. When Mike pulls up, two doors and three windows at regular distances can be seen. The interior however only shows a single door and two windows at varying distances.
In actual rock blasting jobs, the bore hole is not left open but sealed with concrete so as to stop too much pressure from escaping inefficiently.
When Kim and Jimmy perform the architectural plan-switch scam, all three copies of the drawing are rolled up with the printed side facing inward. Architects and contractors always roll drawings with the printed side facing outward, to prevent them from curling up when being viewed on a flat surface.
Gustavo Fring has a modern, flat Dell LCD monitor on his office desk. These monitors weren't yet available in 2003 when the story takes place.
Cities require at least two (as many as five) copies of architectural plans to be submitted. On approval, all copies are stamped, and one copy is sent to the contractor to be used during construction. Tricking a city clerk into stamping one copy of a different design would not do anything about the other, stamped copies.
It is never explained how the tons and tons of dirt and rock are removed from the site without the use of an elevator.