You know....I had the same problem when I installed my Brazilian Cherry ( 3/4" thick by 3.25" wide) that I purchased from that dreaded discount wood flooring place LL .
I'm not sure if what I did is the right way of correcting this situation....but here is what I did....
I noticed mine on the second row that I laid down....so I went back and ripped it out...yes.....I ripped out almost two full rows the complete length of my house. I THEN MEASURED EACH AND EVERY PIECE OF FLOORING on both end to make sure they were the same AND correct size.
I still ended up with some board just like the one in your picture only to a lesser degree....when I did....I put my nail gun over the opening and HIT IT VERY HARD...and it seemed to suck up well. The flooring that was really bad and not useable for for the main portion of the floor, I used for the outside edges and for the closets and such ( almost a third of 1300 feet of flooring) I then trowel filled all of the gaps....I currently have a a table top floor.....for now.....