Sometimes I think the Band just fails to get a lock at those intervals after the workout for whatever reason, but I think the bigger issue is if the Band automatically syncs workout data to the phone too quickly after the workout is completed.
I had noticed back with the original Band that I was getting either no post-workout heart rate recorded or just the 1 minute heart rate about 75% of the time after running. I noticed that if I manually synced with the Health app after a workout that I never got a post-workout heart rate recorded, but often the Band was syncing automatically soon after I ended a workout.
I started the practice of turning off Bluetooth from the Band before starting a workout or turning it off from the phone if I forgot. I started getting the 1 and 2 minute heart rates recorded about 90% of the time when I waited at least 2 minutes before turning the Bluetooth back on and allowing the workout to sync with the Health app.
I haven't been worrying about the post-workout heart rates for the past 6 months or so, but I recently started running regularly again. I noticed this data missing on many of my recent workouts, so I tried disabling the Bluetooth before the last few runs. It has recorded the 1 and 2 minute heart rates every time I've done this recently.
I'm currently using Windows 10, but I also noticed the trend of automatically syncing workouts too quickly with Windows Phone 8.1, and this same trick works for both the original Band and Band 2. I don't know if the Bands automatically try to sync with Android or iPhones immediately after a workout or if this issue is specifically related to Windows phones.