Sometimes frequency separation works in LAB color mode and sometimes it doesn't. When it doesn't, the high pass filter also malfunctions, both generating a high frequency layer that is an inverted version of the low pass layer. I've had it stop working on the same layer in the same file before and restarting the app or even the iPad doesn't fix it.
No idea what causes this, haven't been to determine a trigger, but when it works it works on any layer in any file, and when it doesn't it fails on all layers in all files. Seems to be limited to LAB as I've never seen this issue in any other color mode.