I'm running EKOS 3.5.0 compiled from source on a raspberry pi 4 8 GB (64-bit ubuntu mate) and experienced the same.
I was about to take flats, and all tickboxes for focus was unchecked in the capture menu. The first thing Ekos did was to call focus upon filter change.
Changing focus when taking flats is probably not what we want.

Else, I must say that stellarsolver and multistar guiding is working really great. Great work!

ASI1600mm Pro, Zwo EFW, Zwo EAF, GEM45.