Invisible lines showing and Disappearing in InDesign when Printed

This problem does not happen in Adobe CS4 products and I recently switched to Adobe CS6 indesign and photoshop. I keep running to many problems (well its more than when I worked with CS4 products).
I'm asking this because clients keep sending me horrible 72 dpi rasterized files. How do I deal with it if the program deals with this differently?
I know this has been asked before I think but what if the files are coming from the client's side?
The left circle is the original pdf file the client has sent me. The right circle is when I placed the file in Indesign CS6.
Except that the logo is rasterized. The rest is vector.
The left is rasterized, exported from indesign using 100 dpi. Usually my customers send in files that are 72 dpi. And then I have to manually create bleeds on them. The right is an exported pdf.

What are you expecting? The original files you're getting are not suitable for print.
that said, how are you outputting these files?

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