User blog comment:AgentG231/What specifically is the bug in the Animus 1.28 that made Altair can't swim?/@comment-4699238-20130425063554/@comment-5088097-20130425064141

That would be a fine explanation, however, if you check the trivia section of Altair, as well as reading the manual of AC2, you'll see that it's really a bug. Also, he's an Assassin, hence needs to learn survival skills, so that included swimming.