Hey Faisal
OK, then it looks like that these phages did come from your samples. I googled Leuconostoc and it seems that they are associated with milk, cheese etc
Anyway, that being said, I would align the primers you used to amplify the ITS library and the Leuconostoc phage sequences to see if they indeed can amplify the phages as well. My guess is that they did but just to confirm.
Then if indeed what happened is that your ITS primer accidentally amplified phages as well, I would suggest to try and remove these phage sequences and then work with the rest of your data…