It happens now and then. To lots of CMDRs in lots of systems. I suspect that it is to do with server load. The worst example I had was having to scan 7 times before it actually completed the scan. There are also similar issues with blowing your horn. You frequently get an incorrect scan, even with the Advanced scanner. Blowing the horn again usually works, if you leave it long enough. Again, I suspect server load. I sometimes get,say, just a star and two asteroid belts shown in the system scan, with a gap between the belts that obviously has planets in it - very like the view you get with an incomplete scan from just a basic scanner. I also get it where you blow the horn and are told there are lots of objects (say, 54), but the system map only shows a couple of stars, or similar. Blow the horn again, and it reports the 54 again.
Bottom line is that it looks like server load problems, with the client apparently not knowing that it has only received partial information: not only do you need to worry about the server loads, but you should probably put in more robust comms wih the server, so the client knows when it has only got partial information, and asks again.
TL; DR : scans are inconsistent, do not always work, and often report wrong information.