I have the same problem. I can start the swapfile normally with herd start swap-/swap/swapfile, but it fails to start at boot.
Here are the (possibly) relevant parts of my system configuration:
(mapped-devices
(list
(mapped-device
(source (uuid "59d615e4-8a35-469c-aa24-88f28f084847"))
(target "ex")
(type luks-device-mapping))))
(file-systems
(append
(list
(file-system
(type "btrfs")
(mount-point "/")
(device (file-system-label "ex"))
(options "subvol=guix")
(dependencies mapped-devices))
(file-system
(type "btrfs")
(mount-point "/swap")
(device (file-system-label "ex"))
(options "subvol=swap")
(dependencies mapped-devices))
(file-system
(type "vfat")
(mount-point "/boot/efi")
(device (file-system-label "EFI"))))
%base-file-systems))
(swap-devices
(list "/swap/swapfile"))
Let me know if I should include more info.
-Zacchae