I was recently playing MW, and I saw a rat on the road in front of a tree, I went up to attack it, and went it leapt at me, it disappeared! It continue to attack me however, and when I went into the console and clicked in its direction it came up with the usual; ""Rat"" ; So it was invisible, is this a bug, and how can I fix it?

There's a slight chance that the rat glitched-out and went into the ground, yet was still able to "attack."
Unless this happens often, I would just forget about. Morrowind is a glitchy game. Funny things happen sometimes.

If it does keep happening, it is likely some sort of weird mod conflict.