I've had this niggly little issue for some time now, and it tends to rear it's head once every 5-10 min during each Glyphs session. So not huge, but I definitely notice it.
Basically, I will be using Ctrl or Cmd plus my arrow keys to adjust L/R sidebearings. I haven't been able to reliably reproduce the issue, so I'm unsure about the cause, but the shortcuts will stop working, and I get the system error 'boop' sound, as if the glyph I'm adjusting has lost 'focus', and OS X is unsure what I'm trying to achieve that with particular keyboard shortcut (and so returns the boop sound, with no action).
It happens more often when I'm doing a lot of spacing, so continual/repetitive use of these keyboard shortcuts. The fix is easy, I simply have to use my mouse and click back on the glyph I'm adjusting to regain 'focus'. Then the shortcuts work just fine, until the next time the issue happens.
Anyone else experience this? Let me know if you need more information from me.