I have tried to replicate the scenario that you described above. I have created a bot named "Milk&Dung" that follows your steps within a "Repeat Forever" loop, as shown below. It will find and pick up a bucket, find and milk a cow, move to and add the milk to the Milk Storage, drop the bucket, find and pick up a dung, and move to the Compose Bin and add the dung.
I then changed the focus to look at your posting. Because I always use "windowed mode" in Autonauts, I could still see the steps that the bot followed while the focus had changed, as shown below.
Although the bot some times needed to wait at the "Find nearest Dung" step until a cow had dumped a dung, it would continue to follow all of the step as long as there was room in the Compost Bin. When there was no room in the Compost Bin, the bot couldn't add the dung and so it would fail several steps. Perhaps that might be similar to what happened with your bot. Since you said "Trying to pick stuff up with a hand that should be empty", maybe you were implying that there was a failure when the hands were not empty. If so, I can understand that the bot would fail there. I would view that as an opportunity to try to find a solution (perhaps using a "Repeat 1 times" loop with the test-for-failure option checked).
Good luck.