Yes, the negative exp is part of the new exp system, it's because the evolved form of a pokemon has a higher base exp than its earlier form, and the neagtive is the catchup to what the evolved pokemon should have needed to be at that level. Any pokemon from before the exp system was changed were also effected, and as they now need more exp to level, have negative exp too.
The level cap was also reduced at this time, and has been slowly raised over time to prevent any speed hackers or the like from having full PCs of max level pokemon weeks before other people had levelled their pokemon.