I've seen exact;y this effect, even though I have branching = 0 in my config file - so ordinarily no chance to have two
 replies to an entry.  My pointer aka mouse (I'm on Linux) is a bit dodgy, and sometimes disconnects/reconnects, so in effect gives a very fast double click.  I've always assumed that was the cause of the problem.  The two replies have incremental IDs, and both those IDs are listed in the "Reply to" header section of the entry.  I'm not sure how this overcomes the branching = 0 detail, though.

That is what I have assumed, but if others see this on occasion, perhaps it's got a different cause.