I used to use the dishwasher to clean my wine bottles, but then noticed upon closer inspection specs of sediment in a few of the bottles. Water/crud gets in, but is not always able to get out. So, despite using the dishwasher I always had to check each bottle still rinse a few.... I think the sediment would either be minerals or old soap/food that was in the dishwasher from prior washes. Make sure you clean the filter out at the bottom of your dishwasher!
Now I just avoid the dishwasher all together to save time from checking each bottle. I rinse the bottles immediately after they are empty, soak in oxyclean, and rinse with bleach or star san (depending on what i have on hand) before bottling.