The Apollo Service module was painted with an aluminum paint. Aluminum paint will bubble severely if exposed to temperatures above 747 K, if properly cured. One can only assume the paint was exposed to something close to that temperature at some point in it's lifecycle.
Tracing back, let's see where we can find them. Here's a picture of the SM from the LM after release around the Moon. It's hard to see, but I think I see some evidence of the bubbling near the CM, where there's high glare. This matches the same spot as seen at your image.
The breakdown of the spacecraft is as follows. Note that the image was almost certainly taken from the side hatch.
If I had to venture a guess, I would say it probably happend when the tower was jettisoned, some small flame reached the paint that caused to to boil somewhat.
The next image is at the Rendezvous, post-Lunar mission. There is certainly bubbling seen there.