When you supply a reactor via a TE item duct (Could also affect other item transport systems but I haven't tested them) the reactor will take the ingots even when the reactor is already full.

Version 2.14A

Ok I have tested this further and found, the ingots indeed leave the storage container destined for the reactor.
However they stack up at the input valve.

So I guess this becomes a question, is the input valve meant to act as a full stack inventory?
Or should it only take ingots when the reactor itself has space for them?

P.S. Love the Mod cant wait for the 0.3 updates

The access port can indeed hold up to 64 ingots of fuel, and the reactor will use those ingots as needed. That's intended behavior.

If you break the access port, you'll still get your ingots back, so there's no harm in leaving some ingots in there.