I've passed 1000 passengers twice now in the Berlin Grey Lokomotive Achievement... using the "relief line" strategy recommended in the Steam Community... https://steamcommunity.com/app/287980/discussions/0/458606248618313879/
For some reason, minimetro did not recognize my achievement either time. The first time I thought it was because of overloading the "relief line" -- installing it somewhere else, before the lokomotive reached the end of the previous line location. (This causes a spare lokomotive to immediately start, while while another lokomotive runs out a remaining segment). The second time, I made sure the lokomotive popped back into my inventory before I reused the relief line.
I've passed 36 of 37 other achievements -- I think I understand achievements now. So what's the story? Are there any unstated conditions? And are you sure there isn't an error in this achievement checker, or the wording for Grey Lokomotive achievement?