1. Repeatedly receive reward from Saurid for destroying the Chitik base
Edit: FIXED with 1.0.13c
2. Commodore dialog is stuck, cannot get crew members
Edit: FIXED with 1.0.13c
3. If first encounter with Phage is when they warn you not to approach their planet, then afterwards they refer to a topic never mentioned before (like hand over a crew member?)
4. Encountered phage, surveyed all of their space and found an ooze sample (using a drone), then came back to Kite station and Pilman gives a quest for a sample without noticing it's already there and cannot be found again.

Partial work-around :

Go back to Phage Prime and loot the laboratories.
3 away missions, loose 2 crew on the last one.
With the data from the 3rd away mission, return to Kite Station, talk to Dr. Pilman, do the research.
Go back to Phage Prime and do one last away mission.
Then kill all Phage ships, no more Phage ships spawn in after that.

Go to Red Sea, can get to the 'just under the surface" location now.

There is some bug with the achievements that's connected to game progress. The dev pushed an update immediately, but GOG has not updated the offline installer yet. I'm waiting for it too for my second playthrough. It's available through GOG Galaxy though.

thx for the workaround!
Probably the "sample" I found was something unrelated to the quest and misleading.

The update is now available (1.0.13c).

That's great! You might still have to go back to the Phage world. Read carefully the quest prompts and the interactions. Use the search in the mission log too to look for other logs with "ooze" in them, for example. It's really helpful for most missions.

I had GOG Galaxy on during my first playthrough, so I didn't encounter the bug, But I did complete some side quests without following the "proper" steps and I had 2 pending mission notifications for already completed missions at the end of the game. This game really doesn't like if you do things out of order and it's experience breaking, so I hope there are more updates coming.