I have tried to reproduce this issue but failed. It could be a has a chance of theme or plugin conflicts. You can disable all your plugins except User Frontend and switch to a default theme of WordPress like- Twenty Twelve, Twenty Thirteen, Twenty Fourteen and let me know the results.
Yes, you're right. I switch to dokan theme and there were no problems to update variations. But I have to use my Mindig theme. In your opinion, what could be the problem and how to fix it?