After they finish doing the fillings, they file the new material down to fit your bite. You might recall them having you bite down on a piece of paper and then they'd sand away all the parts that were hitting. The more fillings that get done at once, the harder it is to get this done properly, I think. If certain parts of your filling or teeth are hitting before the other parts are when you bite down, or if they are otherwise not fitted well, it can cause pain throughout. (They are also more likely to fall out then)

Source: Personal experience with bad fillings.