To answer your general question "What should I do?", I would submit that it's not that big of a deal, it will probably be fine, and only you will ever notice that the tenon on one end of the bench is fatter than the tenon opposite. Since you haven't cut the tenon yet, widening the mortise seems like the easiest solution. If you're not already planning to peg it with drawbore pins, you might want to consider that now. The point is to hold the tenon tight in the mortise. Drilling a hole perpendicularly to the mortise, straight through the bench leg and the tenon, then pegging it with a piece of oak dowel, should do the trick. For an even tighter joint, offset the hole through the tenon about 1/16" from the hole through the table leg; then the peg will draw it in tighter. It's not so important to immobilize the tenon from potential left-right movement, so I would disagree with the answer that suggests you need to fill the gaps with epoxy.
To make your mortises line up better next time, make sure you're marking the distances off the same face of the leg. Rather than trying to eyeball the center of the leg or even measuring precisely where the mortise "should" be based on the leg's dimensions, use a marking gauge or square and mark off the distance from the reference face. In other words if you're marking the mortise on the "east" and "west" sides of the leg, make sure both are measured from the "north" face rather than marking one off from the "south" and the other from the "north".
