There seems to be some funny math going on with the shops. For example, right now I have a reputation of 46 at the Citadel. If I go to, say, sell some padded armor (value 100 gold, sells for 50 gold), I get the full 100 gold when I sell it. Assuming reputation affects vendor prices, this could just mean that it's not displaying the reputation-modified sale price.
Similarly, I've seen items for sale that have the "not enough gold" icon on them, but that I can afford. Again, if reputation affects prices, reputation may be influencing the cost, but not being used in whatever logic check determines whether to show the "not enough gold" icon. See below:
Anyway, sorry if I'm being nit-picky. As a hobbyist programmer, I tend to zero in on the math/logic bugs.