"We've been having the exact same issue. On our Xperia ZR there were no issues with focus but since the Z3/Compact have come out Sony seem to have changed the camera libraries, and there are some issues as a result.
We've tried to mitigate the issue in our latest update. On the Z3 Compact you could try a resolution of 720p, a longer interval and leave the default focus as it is.
We'd love to see your timelapses without the refocusing. Please let us know how you get on.