There's sort of two issues here. One is catching the defective rounds through inspection. The second is what's causing the lack of powder in the first place.
The same thing happened to me. One here, one there, then it hit about 10%. I had great difficulty visually inspecting cases because of the small charge in the .38 cases. I really didn't feel like dumping my Dillon and completely changing everything after 30 years of no problems. I just needed to figure out what was causing it.
I finally figured it out. The spring return on the Lee Auto-Disk I used was failing to return the disk. It's hard to spot with the black on the black housing. I put a colored sticker on the side of the disk to help me spot it's position.
I tried all sorts of things to correct the issue, to no avail. It even failed on a completely different Auto-Disk. I came to the conclusion that the spring return system is just not reliable. I figured a way to mount the chain they give you as an option which drives the disk closed.
If you're using a spring return Auto-Disk, that might be it. I used the spring for years with no problem. The it went south on me. A search of different forums tells me I'm not the only one this has happened too.