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I had the same experience in one of my game. No anomaly, colonized system or anything that should not have my starbase collect the trade two hops a way in this one system while it could do it in others.
I then build a station one hop away instead of two and build a trade hub and I manage to collect it. Pretty sure it is a bug.
I would report it and apply the save.
I had a few too many mods so I didn't think it worthwhile to do that.