Odd Bands on Gel - (Nov/15/2012 )

So, I performed a gel electrophoresis after gel extraction to determine the concentrations of my PCR product and vector. When I viewed the gel, both bands were at the right positions but one looked to be almost half a band. What could be the problem here? Could I not have mixed the loading dye with the DNA enough?

Half a band which way? As in less thick that the first band? Or do you mean it doesn't go along the whole width of the well?

Could you post up a picture?

Doesn't go along the whole well.

In that case it is quite likely that you accidentally punctured the well with your tip when loading, "injecting" the DNA into the gel rather than letting it fall into the well.
Alternatively, there could have been a fragment of gel left in the well when you pulled the comb out.

I doubt very much it has to do with loading dye mixing, if you didn't mix properly the consequence would most likely have been a fainter band (as you would have potentially lost some DNA into the buffer).