| Some puzzles require you pressing down the mouse button, not just clicking with it. Such are all light-bridge repairing puzzles and crystal-lighting (in the room behind the airlock)|
To retrieve the lens that you find in the lower part of Nexus, use the control panel and first try to find out what each button means (don't forget to exit the console and press the triangle button for the droid to work). Then it just takes a little adjustment to make him retrieve the lens for you, typing a combination of down, right, and stop (red button). To put the lens in its place, don't forget to input several "up" commands first, as the drone starts its movements in the lower part.
In order to repair the light bridge on Map Spire, you should adjust the prisms in such a way that the light goes through all of them, and the colored lights touch the correspondent colored buttons. This is easier said than done. You should try turning the source towards all the prisms, turn the prisms themselves and find out which is the one that makes them all lit (it's the lower one, when turned three times). Then just turn two other prisms to adjust the colored rays, and the job is done
To catch the critter in the Planetarium Sphere, make a trap (with the wheel, the rod, and the cage - that's an easy puzzle), then click on the holes until Boston says "Something is moving in there!" Then quickly stand between the wooden wheels, to prevent the animal to escape to the left. He will run out and stand near the trap. Then just click on the trap.
The turtle puzzle - that's a tough one (see image)!
Images: (click image to see larger version)