You said "I just updated...". Does that mean you downloaded a newer version of Autonauts, or does that mean you just loaded a recent save file, or does that mean something else?
If you downloaded a newer version, which version did you just download? If you think that the newer version might not have gotten installed correctly, I suggest that you read this posting for instructions on installing the downloaded file: https://itch.io/post/475749
If you just loaded a recent save file, perhaps that save file is broken somehow. I suggest that you try loading an earlier save file that you had loaded before and which you were able to use without this problem.
If you mean something else, please clarify what happened.
I also suggest that you take a screenshot of your game while you are pointing at the ‘unusable tree soil’. You can take a screenshot by pressing the "PrtScr" key - you might need to also hold down another key such as "Shift" or "Ctrl" or "Alt" or "Fn". You can then open Microsoft Paint and paste your screenshot there, and then save the file in Paint with extension .png. You can then come back here, enter your reply, and click on the "Add Image" icon just above your reply which will allow you to upload the .png file.
Once you have given us some more information, we may be able to help you more.