It seems that when deleting a stash in GUI, it is being deleted based on it's position in a list. So if have 3 stashes (let's call them A, B, C), this will happen:
1. I select the first stash (A), right-click delte stash.
2. Operation, takes a while to process, in the meanwhile I right-click and delete the second stash (B).
3. What actually happens is that stashes A and C get delete, while B stays.

Additionally a similar problem happens if I delete B and then C, I will get error message about invalid position.