Dear Elif,
I also work at a flour mill. The whole milling process is based heavily on sieving, in order to have an adequate particle size, while also removing as much bran as possible. So, at least in regards to physical contaminants, you´re covered by the cleaning process: scourers, separator, pneumatic removal of light contaminants, magnets which are there mostly for the sake of not ruining the rest of the equipment, but likewise a great aid in regards to food safety. Then, flour has to pass 100% through a 180 micron mesh. I would start looking after the sieving part. Your mill probably has a turbosifter before packaging, maybe a magnet. These would probably be your PCCs.
Turbosifters have openings that are 2 mm in diameter, so they reject anything larger. According to the US FDA, physical contaminants must not be between 7 and 25 mm.
Microbiology would probably not be an issue, since humidity should be under 14.5% for flour. Although millers would like to have more humidity for a better yield, this also means that flour gets stickier and would cause certain pieces of equipment to clog up.
As for chemicals, like pesticides, I agree that you should control it by having certified providers, since it is very costly to test every grain lot. How often have you found fuel in your grain? Is this usual in your country? If that were the case, you do need to have a way of dealing with the contaminated grain, so you would have to test for this much more often.
Hope this helps.