Don't you rotate the hub forwards (in the direction the chain will drive it?) This is important because lacing a rear wheel assumes forward twist because otherwise the spokes will cross at the valve hole (instead of being parallel) and interfere with pressing on the pump chuck.
Possibly a few nipples are hanging up and not fully engaging in the rim's spoke holes. It can take a bit of shaking and coaxing to get them all drawn in as you twist the hub.
You don't screw the nipples all the way down at this stage of the build -- just four turns, enough so they don't fall off while you're finishing the lacing. This should give you enough slack to get the next 16 nipples engaged.
Otherwise, if you are sure the spokes are the right length, you could have made an error in the spacing of the spokes as you went around the rim installing them. Or you might have mixed up the offset in the spoke holes in the opposite sides of the hub by getting one-backward instead of one-forward.
Occasionally you will encounter a hub where the spoke holes are not offset but exactly opposite each other. Use these for making paperweights, pepper mills, or mobiles, not for building wheels.