Ive been struggling with an idea for a while now, and in no way can i make it work but if you could it would explain the neo/smith ending.
Smith triggered the emp, and possible that was at exactly the same time neo looked at the squiddies, hence somehow they were effect by the emp through the neo/smith connection
obviously the timeline doesnt fit and the whole neo smith connection transfer thing is complete ass but yeah :P
When neo was running from the squidies i nudged my mate and raised my open hand, jus before neo pauses and does exactly the same, got some geek cred for that one.