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.

Go into ATO>Configure Excerpts and experiment with the "Don't strip these tags" feature.