I am new to Atahualpa and just installed 3.5.1. I noted that excerpts have unusual characters represented by a little square. This is often when I entered multiple spaces. To get rid of the little square, I had to delete all of the white-space characters and then add one. It is as though WordPress or Atahualpa added a special version of the space letter because html expects one space and ignores multiple spaces.
Assuming that the odd character is %nbsp, then three spaces yields " %nbsp ", and four spaces yields " %nbsp %nbsp". That is, there is an algorithm to add a character that the excerpt display code interprets incorrectly.
The special space characters that cause problems in excerpts do not appear when viewing the same text in "full page" mode.