Question: Why wasn't Castor Troy cuffed to the bed and watched by several agents? And how did he know which agents knew of the switch and thus kill only them?
Answer: For the first question, in the chance that he did wake up (which he did). He's a very dangerous man in a coma and could wake up and escape if not watched or cuffed. Second question, he would have watched the video seen when the doctor comes in and saw which agents were there, as well as would have tortured the information out of the doctor about it.
Good answer to the second question, but the first one asked why Troy WASN'T watched and cuffed. In the film, he wakes up alone and unrestrained.
The medical staff thought that Castor Troy was so far into his coma that he wouldn't wake up, as made apparent when the agent put her cigarette out on his arm. They were not expecting him to wake up.
Answer: It's possible the doctors did not expect him to wake up (at least so soon). Also, when Castor woke up, there were no doctors around, but he was watching a video of the procedure. So, even though we don't see it on screen, maybe somewhere in the video he saw the head doctor and the other two coordinating everything before the part we see him watching. A valid set of questions here, though, is: why would a doctor film all this and then leave the tape around, and how did Castor know where to find it?