When checking into a venue on Foursquare, it can be frustrating to see there's more than one venue listed. With some venues leading to unlocking badges, earning a mayorship, or even a special, duplicates get in the way. Marking duplicated venues is nothing new to the iOS app. In the past you'd have to visit the venues page and then flag it as a duplicate, or you could use Hopscotch if you're a Foursquare "superuser" to mark venues as duplicates.
About Foursquare pointed out a new feature in the latest update to the iPhone app that allows users to mark duplicates during the check-in process. It's a simple solution that's easy to use.
While searching for a venue, you can swipe in either direction on the venue name and you'll see two options: Mark Dupes or Suggest Changes.
Tapping on Mark Dupes will then present you with a list of venues with the same or similar names. Tap on each venue that is a duplicate and then Submit in the top-right corner. This won't merge the venues, but it will flag it for a superuser to merge once that person gets to it in the queue.
Android users, you can long-press on a venue (instead of swipe) to mark venues as duplicates, as seen below.