It looks like some guys at the University of North Carolina (UNC) built a utility to investigate exactly this:
TCP is a classic example of a legacy protocol that gets subject
to modifications. Unfortunately, evaluation of something as
fundamental as TCP's loss detection/recovery mechanism is not
comprehensive. Our aim is to perform a complete realistic evaluation
of TCP losses and its impact on TCP performance.
I rely on passive analysis of real-world TCP connections to achieve the required level of detail and realism in my analysis.
The purpose of the tool is to provide more complete and accurate
results for identifying and characterizing out-of-sequence segments
than those provided by prior tools such as tcpanaly, tcpflows, LEAST,
and Mystery. Our methodology classifies each segment that appears
out-of-sequence (OOS) in a packet trace into one of the following
categories: network reordering or TCP retransmission triggered by one
of timeout, duplicate ACKs, partial ACKs, selective ACKs, or implicit
recovery. Further, each retransmission is also assessed for whether it
was needed or not.
I won't say it is production quality. Previously I've built quick perl scripts to store ip/port/ack tuples in memory and then report on duplicated data from scanning pcap output, this looks like it provides more thorough analysis.