There's a simpler explanation: your brain is associating other environmental (internal or external) conditions with the alarm going off, and reacting to those instead of (or in addition to) the actual alarm.
This seems to happen to me pretty often, given that I'll wake up in "the middle of the night" (usually because I need to use the bathroom, or because I want a glass of water), then check the clock, realize that the alarm goes off in 3 minutes, and grumble about the lost sleep time.
This seems to happen to me pretty often, given that I'll wake up in "the middle of the night" (usually because I need to use the bathroom, or because I want a glass of water), then check the clock, realize that the alarm goes off in 3 minutes, and grumble about the lost sleep time.