There are reports of dozens of people with the same problem since years (Garmin Forum, Reddit, etc.).
Most have a watch and a edge and don't want to wear the watch while riding. Since years this causes problems as in this case heart rate and with it, intensity minutes, are not calculated properly in connect even the activity was recorded flawlessly on the edge with a HR monitor.
People tried everything, shut off the watch or watch/edge connections or tried different syncing methods. Sometimes it works, sometimes partly and often not.
I can not believe that a company like Garmin is not able or willing to solve this problem.
https://forums.garmin.com/sports-fitness/cycling/f/edge-1030-plus/398879/intensity-minutes-wrong
https://forums.garmin.com/sports-fitness/cycling/f/edge-1040-series/307495/low-intensity-minutes