Bottled my second batch of stout, everything went good SG 1.048 little high, kit said it should be 1.046, the problem is that when I went to bottle after three weeks in primary the gravity was 1.028, it was supposed to be 1.012, the beer tasted pretty good but that gravity is so high I don't know what happened. I had very good fermentation for the first five days, I didn't take gravity until the SG, and the bottling because I didn't want to contaminate the beer , so were did I go wrong? I will watch for over reactive activity in the bottle, I would think even with dry yeast (12 gm/2packets) I should have finished the five gallon batch.

With only a 42% sugar/alcohol conversion, I would be very concerned with exploding bottles. The additional simple sugar you added to the beer during bottling will likely kick up fermentation again in the bottle, and it's extremely likely that the yeast will chomp right through the simple sugars, and then slowly continue to feast on the more complex fermentable malt sugars left in the beer. Watch those bottles closely!

Here's a few questions:

Extract or All Grain? I'm assuming that this is an extract batch. If so, I would expect the FG to be pretty close to what the kit says. I certainly wouldn't expect such a large difference in FG in a typical Extract batch. If this was an All Grain batch, there are several factors within your control that will influence the final wort gravity.

Yeast Handling? I see from your comments that you are using dry yeast. What type? Did you rehydrate your yeast in water first, or did you sprinkle it onto the top of the wort? If you rehydrated, what was the temperature of the water you used, and how long between the time you rehydrated the yeast and pitched it? Did you aerate/oxygenate the wort any? Did you use the yeast that was supplied with the kit, or did you go for a different kind? What sort of lag time did you experience?

Ferment Temperature? Did you ferment at ambient temps, or are you using a temp controlled fridge? If ambient, are there large fluctuations in the temperature where you're fermenting (such as near an A/C vent)? What temperature are you fermenting the beer at?