I'm a little confused on exactly where the nbsp character is in your file, or what the problem is. Do you have a sample EPUB?
nbsp did undergo a change in 0.6.1, but I'm not sure if its related to your issue.
Essentially the Qt editor does not work as expected with the nbsp character (the 160 code); if there are any nbsp characters in your file when you are using it (whether in Book View or when storing/retrieving it for Code View) then Qt would convert the nbsp character to a normal space character. This meant that if you use an entity string in your code and switched to Book View and back after some editing, all your entities would disappear because Book View would convert them to the nbsp character and then convert them to normal spaces. This was also true when loading a file as the nbsp characters would get converted to normal spaces.
0.6.1 now converts any nbsp characters into entities when it loads your EPUB/file so that they don't get changed to normal spaces and therefore 'lost'. This is the only character that gets treated as special.
Interesting it probably means you'll see more entities in Code View if you edit in Book View. This is because Book View will insert an nbsp character into the code when it thinks you want one (e.g. if you hit the spacebar twice). Before, when you switched from Book View to Code View that nbsp character would be invisibly converted to a space, and the pretty printing might convert the 2 spaces to 1 space. Now you'll see the entity character that you put in there - but you'll probably end up wanting to do replace to convert the ones you don't need to blank spaces