Sure, sand-through is just as smooth on the wood - as on the CA. Of course, when it happened to me numerous times early on, I was using very fine SP or MM; it didn't matter if it was CA, other or wood, it all had the same feel. It doesn't matter if one blank does it and another doesn't. Sometimes it comes in bunches. I had one particular wood in which the CA was constantly lifting on the ends, leaving a cloudy look. But it didn't happen on other woods. Turns out the very oily wood I was using, AND the mandrel. You didn't say if you were using a mandrel or not. That is usually one of the components in sand through, but not always.
BTW, the reason mandrels are usually a component, is that 99.9% of "new to pen turning" folks start off with mandrels instead of Turning Between Centers (TBC). Being new, subtle pressure difference on the chisel to the blank for different reasons are not noticed, but it DOES matter, or alignment of the head to tail stock, too tight of the tail stock on the mandrel, or the use of other than 60° tail stock in the mandrel cup end - results in minuscule out of round wobble that results in what you have. Another way around it is to use a good set of calipers and measure the build up of CA thickness.
I had that early on and did not notice it at first because I used wax. I had sanded through and while it was still turning, I applied wax. Guess what: The wax over the CA shined just like the CA, and two days later the shining wax rubbed off and exposed area of the blank that had been sanded through. I learned an important lesson from that.
About 1 in 3 of the results of the query below deals with spots on CA similar to what yours are showing. It can be a different reason than that, but the most COMMON problem is sanding through. Your picts are classic sand-through. This has been going on since I have been here (14 years).