it's the same issue with antibiotics what if they kill gut bacteria? The answer is they can and do [1]. My guess would be the changes are actually lower with the bacteriophages as they tend to be more specific in the bacteria they target [2] so if that did happen it probably wouldn't cause a widespread die off as much as kill off some specific ones.
1. https://www.healthline.com/health-news/antibiotics-can-kill-... 2. https://arstechnica.com/science/2021/07/maybe-not-so-fast-wi...