Evolution. Ages ago, when something woke us up in the middle of the night in an unnatural way, it was dangerous and we had to grab a weapon and fight. The body evolved so that it could pull out of SP very rapidly. Your brain is preprogrammed to think your alarm is a threat.

Ways to avoid this are: placing the alarm further away. Your brain can figure out how far away it is and will think of it as less of the threat if it's far away. Also, it will be quieter, quiet sounds are less threatening as well. Also, eventually, your brain will recognize that it is just your alarm and get used to it, that will take a while though.