I lined up the crankshaft pulley (the upper pulley) mark with the rear timing belt cover

We may have a terminology problem in the mix here. I don't understand crankshaft pulley being an "upper pulley". And rear timing belt cover with "dimple" suggest you really mean Camshaft pulley.

But in case you did mean the Crank Pulley marks, here is a possible explanation.

By "timing gear", I think the others meant the Crankshaft Sprocket as shown in the photo. The sprocket mark, when referenced to a fixed mark on the seal carrier are the "real" 0° crank position markers.

The pulley and belt cover marks are just secondary references, and the outer part of the pulley (being bonded to rubber) may have slipped, so that it no longer lines up with the fixed mark on the belt cover.

You will have to remove the crank pulley and lower belt cover to set/verify true 0°. If you find the pulley (Harmonic Balancer) marks have slipped, you should get it replaced before it comes completely separated and does real damage.

But since you didn't give us the year of your 240 (?), this may all be a waste if time if it doesn't have the B230 engine with Harmonic Balancer.