How are you trying to fit the neck to the body, sliding in horizontally - your second picture - or pushing down vertically - first pic?
The neck has a slight taper so you want to be fitting it by lining it up as you have in the first pic and pushing down. Give the kit a bit of time to get used to its new surroundings, temp and humidity make a difference.
If you need to make an adjustment after that, sand carefully as Deddy has said.

Grant