I noticed that in the line window graphs, total capacity can get negative. Without investigating that, I'd say probably when using vehicles with lots of extra capacity (in this case, a line of extremely crowded 1906 tube trains).
Hmm, this sounds like a bug. Can you give a saved game or steps to reproduce?
Some of the (Pewhead) tube lines show this.
http://freakshare.com/files/0biupi8t/new-3.rar.html
I noticed this ages ago and thought it was intended as it is kind of useful. The reason is because the trains are overcrowded, they have no spare capacity, and in fact have negative capacity (they are holding more people than they have space!). That graph usually shows the amount of spare capacity in a line, so overcrowded lines will obviously go negative. I use this as an indicator if a line is being used efficiently (want to avoid wasted capacity being larger than transported as that means they are running 50% empty). Running in negative is good as it means your trains are being well used (lots of profit?) but has other negative meanings (slower speed on early low power trains, worse comfort etc).
It might be good to rename the graph "spare capacity" instead of total capacity or something to avoid confusion.
Score 9 out of 10 for user-unfriendliness, with a perfect 10 only obtainable if the software manages to electrocute the user through the keyboard.