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Got the message that a Dark Monolith was on the map, but can't seem to get my pawns to interact with it. It's there, but invisible except for a continuous flashing light. I can't walk over the area (seems to be a 5x5 blocked off), and no clicky commands to do anything.

And I got a harbinger tree growing on my map and it's at about 50%. How screwed am I when it finishes?

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Could be corrupt files after update. As a starting point I recommend deleting the RimWorld folder inside the steamapps folder.

If that doesn't work, consider whether it could be caused by a mod interaction or not-yet-updated mod.