Hello @Pavel yannara Mirochnitchenko !
I understand the concern since you get a Notification to update VLC but the Store APP is not updated
It is a common thing , the Store Apps could have stayed behind , while the vendor have already updated the Retail version
You can select to remediate the Alert by either ignoring or try to deliver the App as a Download from the recommended version directly from the VLC website. This will bypass the Microsoft Store and allow you to install the latest standalone version of VLC.
I guess you have Intune Active on the Store right >?
I hope this helps!
Kindly mark the answer as Accepted and Upvote in case it helped!
Regards