But keep in mind that this is a very few instances out of literally hundreds of thousands of fields. If this were happening frequently, it would be a different matter.
The conventional wisdom is that the hydrocarbons we are finding and recovering didn't originate in that particular rock layer. Instead, we believe it originated from a source rock (usually a shale) and migrated upward until it hits a layer which it can't penetrate. We look for those seals, and hope to find hydrocarbons trapped underneath.
A lot of things can cause oil to migrate even today. A minor earthquake is a shift of those rocks and it is those new faults that provide a crack for upward migration.
There are any number of such explanations which could account for an old field recharging with new oil from below. In fact, under conventional thinking, it would be surprising if this DIDN'T occur once in awhile.