Staining will highlight any imperfections in the wood. From the photo it looks like something has been wiped across the grain. That could be when you wiped the sawdust away or possibly if you wiped the stain across the grain.
Having a good surface to stain is pretty much essential as the stain will highlight even the smallest imperfections.
Applying thin coats as John suggests is the best way.
Also, don't forget that the wood will age - especially for something left outside - so any imperfections you see now will blend over time.
Matching stain is very difficult. Seriously, I heard of one guy who markets himself as the "Wood Whisperer". When guys start calling themselves a wood whisperer, you know you are getting into the black arts.
Typically the average floor installer will use a wood wheel from his manufacturer and pray.
That said, you will not know how good the match is until it ages a little bit and fades, so you have to give it some time. Basically, what this means is that in 3 months if it still doesn't match you can call the guy up and yell insults at him.
You cannot "fix" a stain. You can try re-finishing, but you are rolling the dice even more on that one, because then the wood wheel will not work anymore. The wood wheel is only for fresh installs. Refinishing requires a "wood whisperer". Also, refinishing is expensive because it involves sanding.
Note that finishes can vary under different lighting conditions, so that a finish that matches in daylight, could look totally different at night under incandescent or fluorescent light.
Best Answer
Well you can do one of a couple things.
Stain the entire board. This may be the easiest option, just clean up the drips down the side a bit (sanding them). Then stain the sides and the back side of the board as well. Rub it on, let it sit for a couple minutes and then wipe it off. Unless of course as Keshlam mentioned you are working with a stain/sealer combo. For reference stain sealer combos tend to fade much faster and protect for far less time.
If you don't for whatever reason want to stain the entire board simply sand the sides down and you're done. It shouldn't be too bad since it ran down the sides, should not have penetrated all that much. Make sure to sand evenly along the length of the side (including the spots not hit with the stain).