Are you extremely careful about making sure that no magnets from other devices /cases touch the screen? If those spots are caused by magnets, they should clear up on their own after a few days with no magnets touching the screen.
Source: I bought a third party case that said it was for the remarkable but it had magnets in the cover. These caused warping like you're describing. After removing the case the spots mostly cleared up in a day or two
I'm pretty careful, I don't take my remarkable out and about, and I use the book cover from their store. It's been a few days and it doesn't appear to be clearing up :(
I haven't experienced this, but I've seen several posts here from people who have.
If you have one of the reMarkable stylii which magnetically attach to the tablet's right side, you may be able to slowly "wipe" the stylus across the display several times to "reset" any static magnetic fields which may have built up on the screen over time.
There are also "degaussing" devices for sale on amazon which can do the same thing, however some of those are a lot stronger than you would need so if you do this, be careful not to cause more damage than you're trying to fix.
The marker wipe is not a bad idea, I might give that a try. I'm too nervous to try any stronger magnets in case it damages the device. Thanks for the tip!
I found it to be caused by a loose stylus pointer. Reseated the tip and it worked better.