We've found 18 so far, if you count the Gray Army Base.
1. Dude's House in the Upper Caves
2. Gray Army Base
3. SGS (8th floor, agronomy, in the storage room)
4. Camp Hathor (behind a broken fence south of the docks)
5. Junkyard (in the alley)
6. Rail Crossing (near Buzzer's shop, behind some boxes)
7. Free Drones Base / Underpassages (one screen south of the entrance to the Free Drones base)
8. Foundry (where Everard's sniper rifle is)
9. Core City - Entrance (in shack near train)
10. Core City - Merchants / Hardcore City Bar (in a little room beneath the bar that is accessed by a ladder north of the Doctor's office)
11. Core City - Black Crawlers / Silver Hand Base (in a shack south of the base)
12. Core City - Your House (in the basement)
13. Upper Underrail / Institute of Tchort (in the passage beneath the train station)
14. Deep Caverns Elevator (lower caves south of Camp Hathor)
15. The Rig (2nd floor, room 3, underneath Dude's rug)
16. Oculus (mainframe level, back wall)
17. 3rd floor of the tower at the Aegis Sec base in the Black Sea (1 floor below Yahota)
18. The Pirate Base / Port Ceto (in Katja's Homestead, next to the glowing plant near the exit)
So far, we've found rifts at all of the faction locations and all of the major stations in the game except for Fort Apogee. I've searched all over Fort Apogee, but have yet to find something. It could be that the Institute rift is the only one for all of Upper Underrail (which, given how small it is, wouldn't be surprising).
If anybody has found any more, feel free to post below.
EDIT: Updated the list to include more rift locations. Thanks to everybody for your help!