It's a common bug that I have seen many times in the past, but it looks much more persistant now. (aka it always goes into effect)
To clarify this bug, the points are actually invested in the wonder, but the wonder UI doesnt update, it will only update once you leave the owners city and then return.
Once you return the wonder UI is updated with the new statistics, untill you put more points in it off course.
Closing and reopening the wonder doesn't work, you really have to leave the owners town first.