Hmmm it worked fine with me when I send it into a Space Junk well and an Asteroid Belt. Also, the colonize ability didn't have any issues with me either. I'll make sure to have a closer look at it, though. Thanks for telling.

Already checked

It is set to colonize/extract automatically, the buttons are enabled, there is full antimatter.  I let him sit in the last well for a long time and he just sat there.  I noticed this issue once before in the Diplomacy Beta I think.

I'll set it up to happen again and see if I can get a video of it with Bandicam.