I'm pretty sure that Sarine is the only elf in the vicinity, or at least the only one following Meji and Jon. I'd be asking the same questions Jon is in his position. Just the one elf is enough of a threat to concern me.
As for the SEP field, it works most of the time, but it's relatively easy to see through. Ford saw the bistro-ship because he was looking for one/was more than slightly insane. Arthur saw it because Ford pointed it out to him. Now, as for why the idiot suffering from Vertical Hair Syndrome saw Ellis, there are numerous explanations:
1) He had no idea that Meji used magic to take those guys out. Explosions sending people flying over rooftops and giant rocks falling from the sky to crush people were simply accepted by his feeble mind. Thus it's not entirely unlikely that he wouldn't see Ellis and simply accept a flying, talking, smartass cat. You don't have to be smarter than a wet bag of hammers to get around an SEP field.
2) It could be that he has some inborn magical ability, as has been said. Somehow he had just enough of it naturally that he saw through the SEP. Being untrained and generally clueless, the invisibility spell was totally beyond his ability to detect.
3) Meji stopped diverting power/attention to the SEP whilst smiting the unbelievers, thus letting everyone see Ellis for what he really was.
4) She didn't put the obfuscation spell on Ellis until after the incident in order to avoid attracting any more attention than she already had.
As for the guy in the back, that isn't Jon's twin brother. It's this guy:
http://www.exploitationnow.com/babs2-4.html. Happy Kat sent him into an alternate feudal era via an ancient well filled with the bones of monsters in order to steal a sacred jewel that would enhance his demonic powers. Fortunately for the fabric of the universe, copyright lawyers sued his beanie ass and the guy was brought back to modern times in our dimension where he was promptly splattered across the landscape by some immortal chick with a knife fetish.