This behaviour can be seen in the attached blueprint or map, in which I only created the blueprint to make sure this was not the fault of any mod. To reproduce it turn the combinator on the upper right corner of the screen on and off to send all trains to the left-most station, on the bottom track detach the locomotive next to the wagons from them, delete the locomotive, or get it out of the way by some other mean, you will see that the last signal that points towards the wagons (the one with two lamps tied to it) will stay red, it will stay red, indicating that part of the wagon enters the block, even if you destroy the last wagon and then place it back attached to the other wagons, however if you copy this setup in it’s current state to a blueprint and paste it, the signal on the pasted version will be green and will stay green even if you replace that wagon, it will also be green if you paste that blueprint without trains and then place the rolling stock by hand.
The stations are placed the way they are, four and six tiles apart from each other alternatively, so that, combined with both of the tiles a station takes up, the space deliniated by them is 6 and 8 tiles, this averages out at 7 tiles which seems to be the space needed to house a wagon that is attached to to other wagons, 4 tiles for the wagon and 3 tiles between wagons. The other tracks do not have this problem, presumably because they have more space per wagon, from stations with gaps of 6 tiles between them, so this error does not push the wagon far enough to reach into other blocks.
Placing stations this way makes it possible to park wagons at certain stations and have the blocks, defined by signals placed right next to the station, be considered empty so that trains can go back to the station and keep interacting with those wagons by attaching/detaching wagons, I use this, in conjunction with some mods that let me automatically set schedules for trains and attach and detach rolling stock, to work with wagons individually, much in the same way a real train station would operate, so this bug makes it very hard to store and take wagons from a track but I’m aware that this is a hyper-specific use-case.
