GasBandit
Staff member
The bug is listed here among others,You need to close it for bad weather, and for nighttime, I don't think you need to pet them before you let them out, though I could be wrong. I think fencing them in is just personal preference though.
I never close the doors at night though, unless it's going to rain the next day.
http://community.playstarbound.com/threads/psa-major-animal-bugs-issues.126444/
(I know it says starbound but it's a stardew valley thread)
and as the later posts in the thread are from this week (tuesday) it would seem to indicate they are still present.