I've noticed that when I try to navigate dialogue and inventory menus with the keyboard things are a little buggy. After selecting a dialogue option with the keyboard WASD keys and E (to select a topic), when the NPC finishes speaking the dialogue menu doesn't line up and when I select another topic the game chooses another one. Like talking to the Solitude Inn Keeper about his pet skeever, then selecting the rumors topic the game thinks I selected the rent a room topic.
When I'm going through the inventory menu using the WASD and E keys and I store or consume the last of an item the game highlights the item above that one, not the item that takes it's place.

Has anyone else had this problem?

Welcome to port-land!

Bethesda claimed to have fixed these menu issues 2 patches ago, but I've found only very minor improvements. This aspect of the game really isn't rocket science (has nothing to do with "how massive in scope" the game is or how "vast the world is"). The thing about crappy interface control is that it need not be fancy, but when it doesn't work it has a really really high P/O factor.

You aren't the only one.

The problem is because of where your mouse pointer is located when in dialogue or the menu. The wsad buttons and the mouse pointer can both be used for moving/selecting dialogue and items, as I'm sure your aware. If your mouse is in the same general area as dialogue options or menu options then the game will highlight whichever option/item is parallel to the pointer, even if your scrolling with wsad.

There is a gray highlight, and a white highlight. The white one is what will be selected and is often off screen, but is what the mouse is parallel to. The wsad just moves the "gray" highlight. So t looks like you've selected rumors(in gray) but your pointer is near the top of the screen/closest to rent a room.

Pay close attention and you'll surely pick up on this. I still select the wrong stuff all the time due to this quirk.

Yeah I get this too every now and again. It's hard not to use the mouse when choosing your option but I found that not having you mouse anywhere near the dialogue options helps.

I am aware of the mouse selection having priority. Thought I had double checked that, but I'll try to pay closer attention. Off topic but does anyone know if it's possible to mod the game to let the keyboard selection have priority instead of the mouse. I would guess that this is something hardcoded into the game.

I'm having the same trouble. When I started playing it was fine and I had no trouble. About 100 hours into the game I started getting different selections. No matter which option I had highlighted and lined up with the little artwork pointer, when I selected (whether by mouse or the enter key), it would jump to the top option. Over and over. I stopped the main quest as it mainly seemed to happen in the secret room in Riverwood. I'll try not using the mouse at all and moving the pointer far away and see if that helps. Thanks!