Were you using Guild emblems to level up your guild or perhaps killing high level monsters that made your guild jump from 1 to 3 or 4, instead of level 2?
I just noticed that if you use a Guild emblem or get high monster EXP on a level 1 guild, or just low levels of guild, and you level the guild more than 1 level at a time, you don't get all the points you're supposed to.
I'll get it fixed and reset all guild points in the next maintenance.