This game is WIDELY criticized for this and has since been patched (via a new Director's Cut version of the game) to fix the oversight. Essentially, thr boss battles were outsourced to abother company, causing them to not line up with the implementation of the rest of the game.
You could make it through most of the game as a 100% stealth/hacking build, but a single boss towards the end REQUIRED some combat abilities in the vanilla version. They've since added environmental aids to keep you from this exact frustration.
Source: i too got EXTREMELY stuck here before they released the Director's Cut...
To be fair: this is a problem with Proton too.