Corrected entry: When Frey places her leukemia-affected daughter in the medpod at the end of the film, the machine activates and reads "regenerating atoms." There are 3 problems here: 1) You can't just "regenerate" atoms. Atoms cannot be damaged (especially not by cancer) and can only be ionised, which is definitely not damage. 2) Leukemia is a cancer of cells, and so there would be no need to regenerate the atoms if the cells were the main problem. And 3) The machine would not just regenerate the white blood cells affected by leukemia that are still in the bloodstream, as that would cause further complications with the patient. It would disperse the majority of white blood cells before attempting regeneration. Anyone who studied stem cells in high school and needed an example would know this.
Corrected entry: There are two plot holes in the factory that Matt Damon works in, where they build droids. There are very sophisticated droids throughout the movie performing several different tasks. So why is he working there where his job is to stamp sheet metal, attach it with bolts, and then move the droids to the oven? Surely a droid would be capable of this work, and with the factory's high level of production they would likely be able to afford a generic one for those menial tasks. Also, what is the purpose of the giant oven that irradiates everything inside? It can't be to temper or treat the metal of the droids, because then you have radioactive robots, which also means this can't be a way of charging up their batteries/ power plant. Plus they're assembled by this time, so it's irradiating the wires, hydraulics, and circuitry as well.