Generally speaking, it harmless for eyes with freckles. Freckles in the eyes is the same as freckles in your skin. They are harmless. But if you find the freckle in your eyes changes their color, size or shapes, you shall tell your doctor. That because it may likely change into another eye disorder. So, if there are freckles on your eyes. You shall pay attention to it.
Usually freckles are on the face because of the strong sunlight exposure or skin problems. However, your problem should be taken noticed which is so weired. You should better go to see the doctor and have a full check on your eyes to see whether there exists the problems.
Nothing dangerous at all! It may be pinguecula, the reason of it appearing is the conjunctiva connective tissue degeneration by stimulation of dust and sunshine or aging. It usually come out by old people and longtime outdoor workers. You may never feel pain and uncomfortable, it also has no affect to the vision. Unless it affect the appearance of your eyes, it has no need to cutted out or take treatment by medicine.