That's right! I just re-read the article. It said he fell from the balcony, they were watching them shoot a few takes of a scene where he was "suspended over the street from a wire and dropped repeatedly to the ground, where thugs pummel him and a rain machine remorselessly sprays him with cold water."
I remember seeing a shot somewhere of him on his back in the rain holding arms over his head, so I guess it's from that. He did look all bruised up in the vet scene, but I'd forgotten about the EW article so I figured it was just from the funeral/bullet train fights.
The EW article also mentions seeing them shoot part of the ninja fight, and described seeing Logan get caught in a net that gets pulled by a scooter. Like with the previous scene, they saw them go through several takes of him being "tackled, shoved into the trap, and dragged along a path covered with faux flakes" (it was summer when they filmed that scene).
Wow, it sounds like they did cut out a lot.