I've seen this too - one particular trigger seems to be upgrading a unit that requires a strategic resource to another one requiring the same resource (swordsman to longswordsman for example) when there are no extra resources of that kind left. I got a message about my iron units being less effective because I didn't have enough iron (which was false, it was 0 on the top of the screen and obviously upgrading a single iron unit doesn't change it anyway) and worse yet, I got the notification spam every single turn.