It sounds to me as though he did not see you. On one of my common rides, there is an underpass just like what you describe....it's not that long, but it's much darker in there than on the open road, and I'm pretty sure that most cars can only see my black silhouette riding through inside the underpass if they are coming up behind me.

What can you do to avoid it in the future? Do one or a combination of these things:
---get over more to the right when actually in the underpass, regardless of debris and dead pigeons.
---Get off and WALK your bike through the underpass, just as you might choose to do at a dangerous intersection. Obviously you'd walk on the right shoulder as far as possible. I assume you'd then be off the lane altogether and stepping nimbly over the dead pigeons.
---Get some serious blinkie type lights for the back of your bike and use them when you are going to be going through that spot.