I kinda had the same problem in the beginning, I had a normal truck stop but attached 3-4 lines on it.
Since there are only two platforms, one filled with wood, one with coal. When either iron or goods came in they would just vanish.
(my guess is that it is noticed by business A and B that there is a free ramp at the truck stop and they ship out their goods A+B, but by the time good A arrives at the truck stop it is already taken by goods B that is delivered there faster then goods A and goods A simply vanishes because there is no more room at the truck stop.)
The game doesn’t count goods that are already on route i guess and don’t reserve a spot on the ramps maybe?
I upgraded to a big truck stop myself with 4 platforms and all is working good now as far as i can tell.
My advice, no more then 2 lines on a normal truck stop and no more then 4 on a large. If u need more stops just simply build a second truck stop next to the other one.
Hope this helps.