Unless you have been rigorous about brushing and flossing, it is easy for a bit of plaque to remain on teeth and become transferred to the Invisalign aligners, which are microscopically porous and press against the teeth to slowly move them into their new positions. Saliva is mostly water but has a small amount of minerals, proteins, mucus, and enzymes that can dry to a yellow color and become trapped between the aligners and your teeth.
Other substances can also stain teeth and aligners, such as coffee, tea, red wine, sodas, blueberries, and tomatoes. So can certain mouthwashes.