In the TMS, Armstrong lost 7-10 seconds to 27 riders, including 4 teammates. It seems like Missaglia let a costly gap open which in the age of automated finish timing was enforced. But I haven't seen this gap mentioned or discussed. In a tour of this length, it could well spell the difference.
I'm reminded of the final stage in last year's Tour, where Armstrong lost 15 seconds because of Julian Usano's gap to Franck Ranier, allowing Ullrich to reduce the gap from 1:16 to 1:01. Not that he cared at that point...