Hello, this might be a new addition, but it seems like Glyphs is unnesting components automatically in 3402. However, this produces serious bugs, since automatic alignment is not disabled beforehand.
Export:
The above result stems from the fact that I have two I components that have #entry/#exit anchors at their bounds. One is used in the Softsign-cy, which again is used in my Yeru-cy, in which there is a second I component. So, when unnesting components and leaving automatic alignment on, the two I components are stuck together.
Please disable automatic alignment for the whole font while exporting.