Is it too late for fruit covers?

Typically the bags would have been put on earlier, about 6 weeks after bloom and before the codling moths are laying eggs. It is possible that some of the fruit you would bag have already been "stung" and have codling moth larvae within the fruit. You could try to bag fruit that don't exhibit stings. Even if you missed bagging before the 1st generation, you would be protected from the next generation of insects later in the summer.

Here is more information about codling moths and bagging fruit: Pests in Gardens and Landscapes - Codling Moth