That happened because closer to two years ago now, every Pokémon's EXP and levels were recalculated on the server, because a fault in experience calculation in early versions of PWO meant a large majority of Pokémon actually levelled up too quickly and did not have the correct amount of EXP, which was also affecting some Pokémon's stats. This meant Pokémon in existing accounts ended up losing levels to bring them in line with the proper calculations. However, some Pokémon didn't lose all the levels they were over by, resulting in them being under-experienced. Modern versions of PWO notice this, and show the amount of experience they are under by as a negative number on the Experience bar (which isn't a very user-friendly way of showing it - and I've complained about this a few times myself - but it works). You have to make up the deficit before your Pokémon will begin to level again.