User blog comment:Suparockr/List of Plotholes throughout the series/@comment-5105853-20120718201252/@comment-1388547-20120719235029

For the Prothean VIs: they're speaking Prothean, and Shepard can understand them because of the Cipher from the first game. (Except Vigil, who learned enough of some modern galactic language to make itself understood to the whole party.)

The catalyst was well-positioned to pick up some or all modern galactic languages from his hiding place aboard the Citadel.

For everybody else, read the Codex entry on translation systems.