The first season (15 episodes) originally premiered on the Antena 3 network, so their season/episode numbering is preserved even though these episodes were later made available on Netflix as two separate seasons. After that, the show was picked up by Netflix and the subsequent episodes will premiere there as season 3. For those episodes, Netflix' numbering will be respected.
This means the show won't have a season 2. For discussion, refer to https://www.tvmaze.com/threads/3146/la-casa-de-papel-money-heist.