ATC + Flight Planner = Crazy results

So, planned a flight from KSEA to KSAN in the A320NX (Fly By Wire)

Route:

KSEA

NUSME

BEAVE

KSAN

I pass BEAVE and ATC asks me to drop down to 15,000. Eventually they give me clearance to ILS 9Y at KSAN via the GATTO transition. I select that in the MCDU and it takes me ALL THE WAY BACK TO BEAVE???

I this thing crazy?

Is ATC WAY too late in giving me clearance (they did it about 67 miles out, which seems normal)?

Am I doing something wrong?

See screenshots.