My Oneplus One, running cm-13.0-20160906-NIGHTLY-bacon, has been in a situation for quite a while that apps, for instance Google Photos, report it's using mobile data even though it's actually connected to a WIFI. This prevents Google Photos from automatically syncing my pictures. The WIFI connection is not set as metered. I'm not sure if it's a CM bug or something as I don't see similar reports on xda forum.
The problem is really troublesome. I was trying to solve it all night. I did a full wipe & fresh flash but it didn't help. I dirty-flashed old builds including cm-13.0-20160730-NIGHTLY-bacon and cm-13.0-20160802-NIGHTLY-bacon, the problem remained. Then I restored a 6/6 twrp backup, problem solved! I dirty-flashed the latest nightly onto the restored backup, everything worked like a charm. It's beyond my knowledge to tell what went wrong but anyhow it's solved and hopefully it won't happen again.
Q & A