I've had a look around for another reference to this issue, but I couldn't find it. This issue only seems to occur for me in multiplayer.
I hosted a game with two friends. There were no connectivity issues or that sort of thing and turns were progressing smoothly with no other obvious issues.
Then we started researching upgrades to building and encountered a rather aggravating bug: Colonies set to auto-upgrade building added the upgrade job to the build queue three times for each building. So if I had one Basic Factory on a planet and researched xeno factories, there would be three xeno factory upgrade jobs added to the queue. Once the first is completed, the building becomes a xeno factory in terms of stats, but that does not prevent it from running through the other two jobs 'upgrading' the building to its current state.
The current workaround for this is to deactivate auto-upgrade and do all construction manually, but that adds extra time waiting for others to finish their turns.
I haven't tested if a multiplayer with just two of us causes only two jobs, but I will do if/when I can nail one of my friends down again.
Has anyone else encountered this issue?