Currently working on a 01-05 Civic with a D17A2 and removed the cam to slip off the timing belt to save time. I noticed after reinstalling the cam and torquing down the rocker train that one of the intake valves is pushed down separate from the other. Forgive me as I'm new to working on Hondas.

Is this something that needs to be addressed? Or am I just being paranoid and its normal from the cam lobe? See attached photo.

 

If all rocker arms are installed correctly, the cam is installed properly and the cam bridge is torqued down, there will be a couple of intake valves and a couple of exhaust valves that are open... so this may be normal. BOTH valves will not necessarily be open the same since you are on the non-VTEC lobes during assembly.

Now, I notice from your photo above that you do not have all of the rocker arm locator springs properly installed, so you may have something making contact with the cam or rockers that interferes with proper operation. From Left to Right, the locator spring appears to be on the under side of the rocker arm oil bar (and thus in the way of other parts in the head), the next one is almost properly indexed but slightly high, the third one is properly indexed, and the fourth (Right) one is facing up and not placed against the spark plug tube.