Swagger's shoulder looks to be up in time for any two-count you'd regularly see in WWE. I'd guess it was either a referee feck-up or Punk calling an audible and asking the ref to finish the match early (which wouldn't be surprising either as Swagger has a reputation for being sloppy and causing injuries and concussions).
WWE still has a lot of stuff built around maintaining keyfabe, like the referee power we're discussing, champions publicly carrying around their belt with them, or heels and babyfaces travelling separately (although this one probably isn't done as much anymore).