When a line's last word won't fit it has to appear on the next line. The remaining words have to be spaced wider to justify the line. At some point any display system comes to grief trying to justify an overly short line. Sometimes the result is a less readable display with excessively widely spaced words and sometimes letters. At other times the line is left shorter than the rest.
In the Kindle there is no hyphenation to help break up words. Also, it only seems to justify using word spacing and not letter spacing. These place some limitations on its justification ability. Amazon has chosen to avoid the excessively wide word spacing that some systems resort to and just leave difficult lines short. This results in much better readability at the very minor expense to "pretty appearance".