Pink marks can be due to any one of the following:
Regrind(only on certain ponies - mostly intense pink or orange ponies)
Stains from saddles/bridles left on a pony for an extended period of time
Stains from other accessories(shoes, possibly certain pieces of ponywear, etc) also left on too long
Actual marker, highlighter, or pen marks
Pony make up(The Perfume Palace and some ponies came with pink lipstick/nail polish, and it’s not uncommon for it to be left on to stain)
Stains from miscellaneous items/products due to play and/or storage
Mold/bacteria(in some ponies - only pink or pink adjacent ponies get pink discolorations)

Marks that have straight edges to them are usually stains from some source. Pink marks on ponies that are not remotely pink or pink-adjacent(salmon, orange, etc) are stains. Obviously anything that is writing or a recognizable shape is probably drawn on and a stain. Mold is usually a dark brown dot in the center of a circle of discoloration.  Often the dot and/or the circle are raised slightly.  Regrind is usually random splotches of varying sizes and shapes. It can be as small as a tiny single splotch up to the entire pony’s body.

Regrind is unfixable and probably will spread. Mold is the same, though there may be some possible ways to stop the spread, or at least slow it down. Some ponies may get regrind so badly, they just completely turn that color. The rest may be treatable with careful sunfading.

It's Secret Wish, isn't it???

G3 heads can be really hard to get off. In your second pic I can see little white specs in her plug holes.

Ooh good eye! At first I thought that might be dried product residue but you're right. I just pulled out my husband's lighted magnifying glass and there's a little bit of sparkle at the roots. I'm going to list her as a de-tinsel.

80 degrees  f

I was waiting for the full specs before I started, then life happened...