uyantepui,
I am afraid you have come across the Live Rectangle bug which is limited to the MAC versions starting with 10.7 and 10.8, but not 10.9 (Mavericks), see this thread linked to below.
https://forums.adobe.com/thread/1595973
So a switch to Mavericks with a reinstallation might be the way to solve it here and now.
To get round it in each case, it is possible to Expand the Live Rectangles to get normal old fashioned rectangles, or to Pathfinder>Unite, or to use the Scale Tool.
A more permanent way round that is to create normal old fashioned rectangles, after running the free script created by Pawel, see this thread with download link:
