Yes, unfortunately it's still here. I had it happen last week with some caretaker drones. They seem even more prone to it than colonists. Thing is, it doesn't always happen. A fix that sometimes works is to empty the crate, then use devmode to destroy it. Next, use godmode to replace it. Then let your pawns refill it.

This issue is something the original author (spdskatr) was aware of on 1.0 and was working on, but never found a solution.

Deep Storage buildings don't seem to have this issue, but their interaction with Industrial Rollers is flawed in other ways.