The sentence clearly said, "...no reason for Shepard *not* to take the squad...". Shepard also went on the occasional mission with only one squad-mate. That doesn't instantly invalidate the other trips where two were invited, which also doesn't invalidate the one trip where everyone gets a shuttle-ride.
Some crew fought back and would have required firmer (still non-lethal) methods to be subdued. 'Blatant' is personal perspective. The entirety of the crew isn't visible all at once, nor is there an available roster to study, so the SR2's compliment may only be guessed by counting bunks in the crew quarters. Hadley was also laid up in the infirmary after trying to protect Joker during the attack, so no, the entire crew did not 'wind up alive and well after the rescue'.
Yes, a few data-pads or cafeteria trays might have been briefly airborne or even sucked into space. However, it's just as likely that some of those things might have means by which to keep them in place - some form of magnetism or likely mass-effect tech. The evacuation of such bits is irrelevant given the need to escape and how quickly the Normandy departs.
These complaints have about as much relevance as re-opening a two-year-old thread.