Hmm ... it looks as though you've welded one of the points from one side of your model onto the other...
One way you could try to get around that is to make sure that all the points that lie along the centre are at X=0, then cut the half of the model that appears wrong (ie: that bit that lies on the -X axis). After doing this, you might need to remove some remaining polys manually.
After doing this, mirror the remaining model across the Z axis (X=0) with merge points selected in the panel to recreate the model.
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