When you put the upper on the lower, push the upper receiver toward the buttstock. The buffer sticks out a little thus pushing the upper and lower off alignment. Stag / CMT guns are very tight when new, don't be affraid to apply a some pressure when pushing the pins in (but ensure that the pin / hole are properly aligned)
The best way assemble the rifle is to put the buttstock on the ground, put the upper on the lower, hold onto the handguard while applying rearward (or downward) pressure and push in the front pin (with my Stag's, I generally have to give the front pin a hard slap with the palm of my hand to get it in).
Once the front pin is in, you may have to squeeze the upper and lower receivers together to get the rear pin in. I have had to do this with ALL of my Stag / CMT guns.
When taking the upper and lower apart (when the guns are new) I have to use a tool to push the pins out as the pins are very tight.
Stag / CMT are tight guns but they will go together. On a recent Stag that I purchased I put some oil / grease on the take down pins because the fit was very tight. With use the parts will break in and be easier to put together and take apart.