But some miner got his low fee transaction, because of the inconsistent relay policies among nodes. That miner rejected the second transaction, found the block, and mined the first tx.
In this case, the user sent low fee transaction first, found out it does not propagate well, almost all his peers reject it. He then sent same coins again, with higher fee.
Yes. It only appears it came after, because no one saw it, until it was in a block (the time of that transaction is the same as of the block it was minted into).