Is it really mind over matter

So I've been somewhat active for the past 11 years (I'm in the Army) but as I gained more rank I have more work and fewer people making me do PT (physical training). This lifestyle took it's toll On me and I'm now on a weight loss / living healthy quest. 
I've never had a problem with our PT test (2min push up, 2 min sit ups and a 2 mile run) but now that I'm working out more often and with more determination I've noticed that during my workouts I feel like death is upon me (I'm exaggerating) and I can't do anymore. I finish out my workout only to find myself way more energized. I feel like I'm cheating myself because I could have done more. I wonder if other people feel this way or is it a mental thing I have to conquer??