I also have this issue (I ended up posting a duplicate bug report for it). . Also using the steam version. /u/gmos described the issue perfectly. I also saw it prior to Space Age, but never got around to posting a bug report for it.

When playing Factorio Space Age on the steam deck, the cursor that is controllable with the trackpads disappears sometimes. It seems especially common when using remote view and adjusting recipes in machines. It appears sort of like Z fighting. It will disappear when hovering over some items in the ...

When Factorio restarts itself (usually through syncing or updating mods) on macOS, it leaves orphaned versions of the game in the virtual desktop menu. I don't know the proper term for this menu, but it is accessible through a three finger swipe upwards on a trackpad. If you click on the orphaned ve...