There are a number of glitches in the Friends System - this might be a new one. I've had a similar glitch where I only get the Friend Bonus on random raids rather than every raid. And I only get the Friendship increased 2 out of every 3 days for some people - then I jump up to "Great Friends" for 5 people all at once. (I wish I could get a warning for this, so I could pop a lucky egg and double that XP... ah well.)
GamePress
Buddy Bonus
Some days ago I did raids in a group. One was a superfriend so I got +1 Ball the first time, but than for the other raids I didnt get the bonus anymore. Why?