One way to reproduce:

var server = MongoServer.Create("mongodb://localhost/?safe=true");
var database = server["test"];

var text = "Hello World";
var stream = new MemoryStream(Encoding.UTF8.GetBytes(text));

database.Drop();
database.GridFS.Upload(stream, "testfile");
database.Drop();
database.GridFS.Upload(stream, "testfile");

The second upload fails because the index on

does not exist on the fs.chunks collection. EnsureIndex failed to create it the second time because DropDatabase didn't clear the IndexCache.