Scratches
As the print head is completing a top layer travel moves can cause ugly lines to appear. This can be caused by a couple of things. Either the head is making an actual scratch on the surface or you are seeing slight oozing of plastic during the travel move.
You can try to enable the "z-hop" feature in cura which will find in the expert settings under the retraction heading: Expert -> Open expert settings... This feature will make the printer lift the nozzle a tiny amount just before making a travel move and then move back down once it arrives at the destination. In combination with this you can increase the speed at which the printer executes travel moves. You can increase the default 150mm/s to 250mm/s without problems. The faster move will reduce the amount of time the nozzle can ooze out plastic. Also consider lowering your temperature to further reduce oozing.
To reduce oozing even more you can set the Minimum travel distance to 1 and set Minimum extrusion to 0. This will force cura to always retract before performing a travel move. This may add a bit of printing time as a retraction doesn't happen instantly.
A side effect of the z-hop feature is that it can leave behind a tiny little blob. However, a small blob is far less visible and easier to remove than a scratch.
This effect is more prone to happen on surfaces which are broken up by holes since the head needs to move around more. "Dreamworker" on the Ultimaker forums came up with a clever workaround to reduce the complexity of the top surface. By adding a thin solid layer on top of the object he was able to reduce the travel moves significantly. The thin layer of plastic was then cut to reveal the holes again.
A little bit more information and another option to reduce this effect can be found here: Getting better prints guide
Protruding axes / Rods sticking out
This can happen if a set screw on one of the pulleys has come loose and it's easy to fix. The image at the top of the page shows a fairly extreme case, sometimes it only sticks out a mm or two and can be hard to spot. Usually a small deviation like that will not affect performance or quality but you might experience a strange knocking sound that is hard to locate. If the rod isn't held tightly in place it will move back and forth with the print head and will make a knocking sound as the spacer is banging up against the side of the machine.
Start by loosening the set screw on the offending pulley fully to make it easier to move. Next push the metal rod back into the correct position. In the image the arrow is pointing to a black spacer, push the loosened pulley towards this spacer until it is pushing up tightly against the bearing. Finally re-tighten the set screw very tightly so that it cannot slip again.
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3D Printers User Guide
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