Maybe it's a bug that the dev's are aware of. It was a bug back in Season 1 and unfortunately it's back. There are only red anomalies in the cluster missions. The cluster sector space is fine though. Do you also have this bug or is it just me?
It's a bug. Same thing occurred during the beta; you would only get the red anomalies inside mission maps, regardless of where it was. They're looking into it; I'll try to find dstahl's post about it and link it.
edit: Never mind, he posted about the bug relating to your level equaling the types you received. I do know that it is a bug (one of those old ones that seem to pop back up occasionally, lol), though, and hopefully it will get fixed soon.