Bug 450746

That's quite interesting if it's always missing the change instead of just occasionally. What I've observed was file trashing in Krusader occasionally being missed even though the operation itself was done by Krusader.
The only logic I suspect to be at play is the time the operating taking affecting the probability of the issue happening, at least it seemed like that the slower the operation got, the more likely it was to still have files left around which are not supposed to exist, and I couldn't see a pattern why some of them were spared, it wasn't always the last few files sticking around. Trashing is relevant here as trash performance scales quite poorly with the number of files, so after filling it up with thousands of files, the trash operation gets really slow.

Upside is that without a surprise refresh, your file cursor / focus isn't getting hijacked. I've had to go fishing in the trash as a result of this odd design choice as quickly deleting files one by one or in small groups with the keyboard only is quite dangerous with the focus being moved once the previous operation is done even though I've already moved elsewhere with the cursor keys.
I've also seen odd file disappearances when selecting other files shortly after issuing a delete command, so apparently there are race conditions which makes your non-refreshing issue amusingly somewhat appealing to me.