I found this one while testing some RF stuff in skirmish mode. This is on the Dec 18 build.
When using different weapons with different RF options the last selected RF option will be applied to all soldiers. If the RF option does not exist for that weapon the soldier will unselect it's RF option and default to the snap shot setting.
For example SMGs have two RF options, 5-shot burst and full auto, while plasma rifles have three, snap shot, three round burst, and full auto. You cannot have the SMGs and plasma rifles both on full auto because it is the second option on the SMGs and the third option on the plasma rifles. When you set the SMGs RF to full auto the plasma rifles switch to the three round burst. When you set the plasma rifles RF to full auto the SMGs unselect their RF options and default to the 5-round burst.
I don't know if this happens in campaigns yet. Also the bug that only lets you transfer 2 to 5 of any item between bases is really harshing my antimatter deliveries.