I bottle as well and all the bottles I use come from a local pub. I take the bottles the day after they were opened, meaning they are fresh. I come home, I pour some organic wash disher in hot water, I fill the bottles and sink them in buckets. They stay like this for 12-24 hours, at which point I take the labels off and then thouroughly rinse the bottles from any residue. I always check the bottles in light, in order to make sure that they are really clean, as sometimes yeast residue/specks can settle at the bottom of the bottles.
I leave them to dry out ( during summer, it's easier, as I leave them in the sun and they will be dried ut quickly ) and then store them in cardboard boxes, leaving a bit of space for air to go in, but no major/big openings, so the bottles do not get exposed to anything that might crawl, fly, etc.
On bottling day, I rinse them with hot water a few times and check again if really clean. I dip them in Star-San, let them drain and bottle essentially. ( I use a bottle rinser - AVVINATORE - and a draining tree for th sanitiser to drain out, although foam will remain on the sides, but that's not an issue )
Never had any issues.