I've seen this happen as well. When gel toys get warm
or above room temperature they can receive color
transfer from things they might be laying against.
Most likely in this case the rubber bands did the trick.
I've found keeping them in a plastc box with lid does well
to keep the usual elements of dust and dirt from gathering
on them as well.
Those too over time can add to the discoloration of gel toys.
Washing them well after use and sometimes even applying a
light dusting of on uncolored/unscented talc based power can
prolong their look as well as their usuage.
As far as being safe to use, yes the discoloration shouldn't
effect that aspect of things.
Also store them in a cool dry place when not in use.
Somewhere that the temperature does not reach excessive peaks
of either hot or cold.
Sometimes direct exposure to sunlight or harsh internal
light sources will also affect the coloration of them.
Here's a shot of a very cool one for anal use I recently
added to my collection.