There is nothing about evolutionary theory to suggest this would not be possible or even plausible. It would be easy for multiple ancestors to arise through similar or even very different means, and subsequently evolve to populate a diverse world. However, this is probably not what happened on Earth. There's too much genetic similarity amongst species to dismiss common ancestry as the best explanation. It's far from a certainty, so it's definitely possible that there were multiple groups of ancestors, but I just don't think it's particularly likely.