Let there be light:
It might be all cool and mysterious to use a dark theme, but believe me its the fastest way to turn away people. Its human tendency to be attracted to brightness and lighted things. The darker you make something, the less time people will want to stay with it. This is one of the foremost mistakes people tend to make. Every colour has its place, and you should be able to judge which colour suits your sites mood.
The combination game:
Its very easy to use every colour in the book, and make your site look all rainbow-ish. However, being a little choosy and thinking about the different colour combinations which you should use on your site will save you time later, and bring in a psudo uniformity. Regularity is something that everyone likes, and if they are faced with similar colour schemes for the same things, it will add to the interface usability as well.
The science of colours:
Apart from the beauty value, there are many colours which universally stand for something everywhere. Take red, which usually means something negative. Something which should not be done, or has been done wrong is usually denoted by red. Green is the opposite. And so are quite a few other colours. Just like in programming, we don't assign a variable true to hold a value false, we don't mess with the meanings of all these colours. Use them sparingly, or else you'll leave your viewers quite confused.
A trick I use is to uniformly divide what colour is for what. A few of them are:
Yellow: Alert, or notice
Red: Negative Alert
Green: Positive Alert
Grayscale Shades: Disabled
You should too keep a list of colours and their functions/denotions with you uniform throughout your site.
Those are some probably elementary mistakes that I have seen people make. I hope you can keep them in mind when you make your site!