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While I was trying to train a basic bot, another bot picked him up and deposited him into the storage shed, now the red program recording window is unresponsive, also, I can't get to the game menu, so I can't save or load or exit, lol.

I suggest that you terminate Autonauts by right-clicking on its icon in the task bar of Windows and selecting "Close Window".  Then, you should be able to start another session of Autonauts.  Next, if you have a recent save file that you made before the basic bot being trained got put into the shed, load that save file.  If you don't, look in the "Autosaves" folder below you "Autonauts" folder, which contains the files that are automatically created whenever you see the piggy-bank appear I the bottom-right corner while the game is running.  Find the most recent Autosave file, and load that file.  Below is an image of a typical "Autosaves" folder which should be named something like "C:\Users\Owner\Documents\yourname\Autonauts\Autosaves".

Argh! Sorry about that. This bug will be fixed in the next version.