@Satsuki yes, thank you! This has been driving me insane trying to figure which mod was causing this but it is happening in vanilla for me too. I have tested this using console commands as well- I am unable to add new deposits to most planets. This also occurs for anomalies and dig sites.
I will test out this mod and see if it fixes the issue.

Hi, quick question to see if anyone else is getting this and if it's ALSO another vanilla problem: When you build arc furnaces now, do you notice they only give yields on planets that already have yields? I notice only a small handful of planets get affected when I build one.