To reproduce this bug use the attached pack. Put it in this folder:

%AppData%\Local\Packages\Microsoft.MinecraftUWP_8wekyb3d8bbwe\LocalState\games\com.mojang\resource_packs

Then go in the game, press the Texture Packs button, select the pack, restart the game, go back in the Texture Pack menu. You'll see that the pack returned back, and selected packs section contains 2 Vanilla packs now. Every time you select a pack and restart the game, one duplicate Vanilla pack appears in selected, but all disappear when you remove ZIP pack from the resource pack folder.