I just played through this game last week. I got thrown off in two parts:
Once was I think after exiting the sub, I ended up going through the sewers twice - with puzzles and bots being there both times! I think it was because I went back to the harbor through the garage after I exited the sewers on the jeep side just to see what would happen. I don't think it was worth it because of the ammo and such that was required to clear the sewer a second time 😀
[possible spoiler]The other was a jeep level where I had to shoot a building to open a tunnel. It wasn't obvious enough in my opinion.[/possible spoiler]
I also didn't get the puzzles in the last level. I know I missed a couple tunnels and a big room but they weren't necessary to complete the level/game.
Don't forget to interact with the DJ equipment in Tech-Noir for an easter egg 😜