That's what's called a real "Botch Job".
Your deck should have been thoroughly cleaned with deck wash and a pressure-washer. Then left to dry completely before any kind of stain was applied. Not to mention those areas were your contractor left the stain, to forming heavy blotches or spots. Any excess stain should have been wiped away immediately.
The only thing you can do now is to sand it down and refinish it the correct way. It may turn out okay but you won't know until all the sanding is complete. To look it's best, you should remove as much of the stain you can. If the old stuff is left on it will show through the new stain, leaving blotchy dark spots in the finish. You may have to hire another "contractor" to repair this "contractors" botch job.
The contractor you hired, should be held responsible for refinishing your deck. If not, Institute legal proceedings and sue that contractor. Sue for what you payed him for the botch job and the cost to repair said botch job. You do have rights and I think you should use them.
The darker the color, the quicker the wood will start to wear, because the surfaces will get much hotter. This is a real consideration if you live in a very sunny region, not to mention the discomfort of walking across dark decking barefoot. If you have a dog or cat, bear this in mind. They are always barefoot.
Sorry about your deck and I hope all turns out for the best.