Dark spots on painted wall
In the original paint job; was the paint thinned before use ? 

Did you use a roller or a brush to touch up ? 

Sometimes paint settles to the bottom of the can:
How old is the can of the existing paint ?

If the can of paint has been sitting - your paint pigments are stuck and coagulated on the bottom and you will need to mix them in. If you have had it for more than 2 years you are better off doing a paint match.  

What you can do is take a piece of paint (a chip) from under an electrical outlet cover to get a match. 

Your lid might have a label with the mix parameters printed on it along with a color sample as well. The mix parameters are the best and the match is the next best thing.

You might be able to repaint over the surface depending on how much darker the paint is. Also remember if the room gets plenty of sun light - the paint can fade and that might be what has really occurred.