Yes there are. But not really because of the ink itself, but because of a reaction of chemicals in the ink to cellulose - one of the properties of paper. These permanent inks use cellulose reactive dyes. As the ink companies say, the dyes are water soluble so there is no effect or damage to the pen. When the ink is in the bottle all is normal. But when the dyes react with cellulose in paper and after the ink dries the ink becomes waterproof and permanent.

A number of permanent inks by Noodler's Ink have been tested as to how they lasted when held under water. Results were pretty good. Each had a slightly different amount of "run".

Oh yes, there is cellulose in those cotton shirts so when you drop these permanent inks on your clothes, well its permanent!

Will inks stain your pen? Some will. Inks in the red, violet and pink colours are more likely to stain the container sectionof the pen. Pelikan Purple will stain plastic convertors to a purple tone. The blue tone inks are generally the least likely to stain, but then again, if you get some of the highly intense colours that general guide starts to fade.