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Besides the trub and whatnot, some of your loss is probably captured in your bottles. Take a bottle and fill it with exactly 12 ounces of liquid. You'll see that point is most likely lower than where you filled the bottles with beer.
you say 2 gallons went into primary. if you left .5 behind in trub that's 1.5 gallons into secondary, now you said you had some trub carryover to secondary so you likely lost another say .2 gallons there and as mdixon points out it's unlikely that each bottle has exactly 12 floz in there.