I have had similar cases where I built by capital city on the elbow of a river and I was able to build docks on the opposite side of the capital from the river, but not along the river itself. It was quite odd to say the least.

I've seen this too. The tiles look like a plain and are next to a river. The when you highlight that tile, it says its a river. Movement through it happens like it's a river.

"I've also seen in .86, a tile that labeled as cliff had some other kind of look to it." This previous sentence I first posted is a mistake. What actually is happening is a plain is south-east of a cliff. When I hover my cursor over the plain, it will say its a cliff. If I zoom in very closely, then it says its a plain.