Unwanted paths showing after cropping to make a repeat pattern tile.

I'm trying to make a repeat pattern tile (using CS5 on Windows 7), but when I crop the pattern, the expanded paths underneath become visible as on the flowers below.
This is what I did after creating the artwork:
Used the rectangle tool to make a box with fill/stroke directly on top of the artboard..
Select all > Expand (selecting stroke only, not fill)
Deselect the cropping box and grouped the remaining objects.
Reselected the cropping box and grouped all objects
Pathfinder > Crop
I'm guessing it may have something to do with the fact I used a gradient on the flowers but have no idea how to resolve it. Does anyone have any suggestions? Thanks.
PS. Please excuse me if this explanation is really poorly worded...I've only ever used Illustrator for fashion technical sketches so my knowledge is pretty limited.

Followed your advice above, and hopefully it will work. The only issue is it's a bit time consuming they way I'm doing it, as I'm having to delete the outermost objects first, then delete any objects which are partially inside the rectangle, otherwise I find some of the objects inside the rectangle are deleted too:
At the moment for the objects that are partially inside the box, I'm using the scissors tool to cut the path where it crosses the rectangle. Is there an easier solution to this problem?

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