When I start a project from “New From Glyph Sets” selecting Arabic Basic and Basic shapes only, the glyph transformation does not work and I get the message as in the image on the link below:
If any other glyph set is added to the initial template (I tested Latin and Hebrew) the problem does not occur.
I have noted this behavior after the last update. I have also recently installed a trial version of Mark Fromberg’s “Variable Font Preview 3”. I removed it when the problem started, but the removal made no difference.
For my month’s worth of a project, I have a workaround by copying all glyphs to a fresh template initiated with an Arabic/Latin glyph sets combination. I hope that works, but I think it is worth that Glyphs look into the problem.