Pine is full of pitch (rosin or tar) and stain alone will never adhere to these areas.

General Finishes Gel Stain on knotty pine.
 

To fix, sand the table lightly with 120-grit sandpaper and restain the table. To improve adherence of the stain, mix 2 parts Gel Stain with one part Gel Satin Topcoat. Apply as many coats of the mix as needed to obtain the desired color, allowing 24-hour dry time between coats.

Note: The stain may never adhere well to the knots because they are too dense to hold a stain. You can try dry brushing the knots with the stain to deepen the color and the protecting with topcoat.