Agent smiths differ from the other Agents

[QuiDormit]

This is the real issue. As much as we like to think big franchises like these are all coherent, they're not. M1 wasn't made with the specifics of M2 and 3 in mind, let alone the comics/animatrix/mxo. These are always things being built on top. Things get a little... sketchier the further from the source they become. What we're doing is taking all the gaps and contradiction and trying to make sense of it. Make theories. Which is fun, but we need to remember there's no magical "right answer" hidden away in some Matrix Bible because really, no-one who made these things thought about what would come after.

And also, sometimes it's hard to step back and realize that what makes sense in our real world isn't necessarily true or logical in the made-up universe of the Matrix. Sometimes, things just kind of happen and there's no need to explain it, you just take it as it is presented to you.

AKA sometimes it's really hard not to overanalyze tings in relation to the Matrix and the universe it's set in.