Issue with smoothing polygon... [I'm a NOOB]

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So I am pretty new to Maya, don't have much experience with it. I have almost finished my character however I have come across a problem when I try to smooth.
To create my character, I modelled it and completed one half of it, I then deleted the unfinished half and just duplicated my good side and flipped it so it was symmetrical. I hadn't smoothed it out to the degree I would have liked it at this stage (as I thought it would be easier to smooth everything nicely at the end), so it is still slightly boxy. This happened very early in my production stage.
I am now almost at the stage of completion and I tried to smooth out my character and something weird happened. It went all weird and I dont know how to fix it other than start again (something I'd rather not do seeing as this is a major school project which I have restricted time on and can't afford to start again).
Is there a way I can fix this? Or do I have to start from an earlier point? :s
This is what it is like before I smooth it:
This is what happens after I smooth it:
It's almost as if my two sides didn't join properly even though I combined them after I duplicated one of the sides.
Any help would be greatly appreciated. I can provide more details if it is necessary since I'm pretty sure my explanation was rubbish.
Thanks.