Maybe, this is VERY VERY odd to me, because I just caught a Zubat too (regular one, and a girl at lvl 7) in my Emerald and it looks fine. Did you catch it with a Nest Ball? Maybe that's why it has hearts (or some kind of 'attract' thing). If not, then I have no possible answer.
Way darker than its normal sprite? That maybe be just a 'dark Pokemon', but dark Pokemon usually don't appear in-game, only in Pokemon XD I think. It's not a shiny, because shiny Zubat is green. Maybe it's a bug in the cartridge or something, because that doesn't occur with a normal cartridge.
That's all I can help with
Source: My Pokemon Emerald.