i have noticed this recently and will accept it if i am told it is because i have installed mods, but i am unsure the mods are the problem because it is the first time i have deleted railtracks since installing them.
i am left with a small circular graphic where railtracks cross roads and if i don't notice and delete them, they cause a problem later with building. also there are 'invisible' things which block 1x1 squares and when i cover the surrounding squares with a road, to find the square in question, an 'end of the line' railtrack appears, but is invisible until i surround it with roads.
anyone else? (would like to rule out the mod being the culprit)