I had exactly the same problem yesterday. Wanted to rebuild my main train line but couldn’t remove two long tunnels. After a while, when pausing, unpausing the game, viewing the tunnels from many different angles and moving the cursor wildly, it was possible to remove both of them, but it was annoying anyway. Actually, this is the first time I had this problem after 140 hours of playing. Isn’t it caused by the latest patch???
Talking about the destruction tool, it’s quiet uncomfortable to use anyway. When holding the cursor over a track you want to destroy, you have to find some spots, where its possible. Moving the cursor slightly (but still hanging clearly over the track) means you can’t destroy it from there. Destroying longer tracks gets frustrating. It has to be possible to destroy a piece of track from ANY point over that track.