I have used Express Scribe for a while from Mavericks to El Capitan. Not that it's problem free (in fact it's full of problems) but the problems didn't seem to get better or worse when upgrading to El Capitan.
I did, however, recently come across a bug where hotkeys won't work on version 5.82. I solved this by downgrading back to 5.77. I can't say if this is specific to El Capitan or just another of a hundred bugs.