Which measurement should I use? In lab, I gathered everything and my partner weighed everything, I didn't realize til now that there is a problem. She measured the copper and the crucible separately, she got 0.89 g for the copper and 11.63 g for the crucible. Those two numbers combined equal 12.52 g. However, when we put the copper in the crucible it weighed 12.54 g.

Which number should I use for the calculation, 12.52 g or 12.54 g?
Given that a 2-place balance is no more accurate than $\pu{+/- 0.01 g}$, you can say that the two measurements were within $\pu{0.01 g}$ of the average, $\pu{12.53g}$, then just use this average for your calculations.