I think it happened to me when I researched the "Urgent AI research" and I had systems already converting with the previous conversion tech.

See here :

https://www.games2gether.com/endless-space-2/forums/114-bug-reports/threads/26557-all-food-and-industry-converterted-to-science-despite-no-conversion-selected-in-construction-queue?page=1

Yes, this is exactly how I did. However only about 20% of the systems suffer from this bug. The rest of them are fine though conditions were similar. Perhaps yours is not the only reason. I assume it also happens if you leave this construction on the bottom of the queue. For example if you've discovered a new technology and instead of removing endless construction from the queue first, you just place the newly discovered technology to the top of queue. Perhaps these options will allow to avoid such nasty bugs in the future.