Flatten an image for printing

I have been working on my logo with Illustrator CC and I needed to print my logo. And I used the .ai file and placed into a InDesign CC document and exported it as PDF for print.
But this is the result of the printed PDF:
and I was talking to the people at the printing place and they said it wasn't flattened properly.  So they flattened it on their printer and came out the way it should.
I used Package feature on InDesign and used High Quality Print preset from PDF presets and I also tried PDF/X-1a:2001 preset too with same issue.  
I was wondering does this feature doesn't flatten images? Or is there other way of flattening on Illustrator or InDesign. My logo consists of lines with stroke.

marrto wrote:
I thought placing a .ai file of the logo in InDesign would be the proper way of doing it.
You are correct about that.
And the lines of my logo are actually a rectangle tool with rounded corners effect.
Okay well, at least that explains the difference between the two images in your original post. The output reported to be "not flattened properly" appears to have lost the live Round Corners effect. A logo graphic should never include a live effect. You could apply Object > Expand Appearance to those elements to make the results of the effect permanent.
The printing company didn't explain it to me very well.
That's true. The term "flattening" was misused.

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