Let me use the graphic I did recently as an example. In the image below, I have used a clipping mask (Ctrl + 7) to "crop" the graphic to fit onto the page.
Let's zoom in on Tevez's eyes. This image below, is the zoomed in version from the first image. The eyes are fine here.
But this happens (below) when you choose to release the clipping mask on the whole illustration.
When I make this mistake, it's not good. I would release the clipping mask because I want to conveniently move some groups of stuff and re-clip back the objects. But I would forget that there are small areas where I've previously clipped. In the end, these areas don't get clipped back.
That leaves me with ball flight lines that should be under the goal post BUT instead appear above the goal post. That's a major factual error, obviously!
To solve this, I've changed to using opacity mask instead. It's safer. But the compromise is you can't move the clipping object easily with your direct selection tool.
The eye white (1) is my clipping object. The pupil (2) is my object to be clipped. In opacity mask terms, the eye white is the masking object.
To use opacity mask, I simply selected the eye white, copy (Ctrl+C) and pasted one in front (Ctrl+F) and push the mask up to the front (Shift + Ctrl + ]). Then I selected it and the pupil together, clicked on the transparency palette options (round button with right putting triangle), chose Make Opacity Mask.
Depending on what colour of your masking object is, you have to check or uncheck the Invert Mask checkbox.
In my case, the masking object is white in colour and I've unchecked Invert Mask