I've had this happen to me on more than a few occasions. Raw hop material can be harshly bitter, so give your bottles adequate time for the hops to settle out.
I did have one beer that was unsalvageable, but that was the perfect storm of bad conditions. I ended up overpriming a bit, so the beer was pretty fizzy. On top of that I used a very flocculant yeast (1968, I think), which all dropped like a stone and stuck tight to the bottom of the bottles before the hops could all settle out. Whenever I'd crack a bottle, the rush of carbonation kicked up all the loose hop sediment off the bottom of the bottle and it would all end up in the glass.
Now my practice is always to stop well short when racking to my bottling bucket. Better to leave a beer in the fermenter than ruin the rest of the case just to get one more.