Looks like Tomato Spotted Wilt Virus is a possibility; what did you notice on the plants themselves? Any leaf rolling, wilting at tops of plants, and/or stunted plants?
As to the fruits -- Any faint signs of spotting on green fruits? Are the patches ever raised, or does the surface of the fruit remain perfectly smooth?
Here's some pics of TSWV that you might want to have a look at:
http://www.ento.okstate.edu/ddd/diseases/tswv.htm
http://edis.ifas.ufl.edu/HS200
(go down to Figures 30 and 31-click to enlarge)
Or it could just be Blotchy/uneven ripening -- but I'll wait to hear more back from you on the above.