The issues are related in that they both are caused from inadaquete mixing.
Not completely mixing partial boils is not a big deal as the yeast will will the wort during fermentation it just prevents you from getting an accurate OG reading. If you really are having problems an option is to measure the OG of the partial boil and then do the math to figure out the OG of the full volume of wort. It's a pretty simple calculation (OG "points" x boil volume)/total volume, i.e. 3 gallons boiled at 1080 would be 80 x 3 = 240/5 = 48 or 1.048 gravity for 5 gallons.
Bottle bombs are a bigger issue as you've probably learned because they lead to exploding glass. Bottle bombs are caused by 1 of 4 problems: unfinished fermentation, too much priming sugar, inadaquete mixing of priming sugar, or infection.
If you used the standard 4-5 oz of priming sugar for 5 gallons we can rule out excessive priming sugar.
How did you mix your priming sugar? Generally adding it to 2 cups of water and racking on top is enough to mix in thorougly, if you're concerned adding a very gentle stir can help. Did you test any of the non-exploding bottles? Were some flat and some overcarbed? Inconsistency between bottles would point towards uneven disbursement of the priming sugar.
Did you take hydro readings 2-3 days in a row until stable to make sure fermentation was complete? If you didn't the beer may not have been done fermenting when you bottled and this could be the problem.
The last potential problem is an infection. Test some of the non-exploding bottles to see if the beer tastes ok, if it does you know the whole batch wasn't infected but its possible one or two bottles may have been.
I guess one final possibility is that you had one flawed bottle that cracked under normal pressure, although this is less likely than the others.
I'd move them all into a plastic container in case they explode again it will be less mess and less dangerous. I'd suspect the most likely cause is an uneven disbursement of the priming sugar. Giving it a very gentle stir next time you bottle or pouring half in the bottom and gently pouring half in when your siphon is half done should solve this problem.