Some files have elements that cause print issues. Some issues we've seen are:
One of the most effective ways we have found to eliminate these issues is to JPG flatten in InDesign. This is effectively creating a screenshot of the file so there are no layers or vectors in the file at all. This isn't optimal for most situations as it increases the size of the file and you lose detail in vector graphics. This should only be done when we're having print issues.
When we have these issues we can do some of this work in house but for documents with many issues needs to be done by the graphic designer.
We used this portfolio to test how increasing resolution affects image quality. We printed this file on our HP Indigo.
Here's a video of the print output. The settings we took a screenshot of are the optimal settings for this particular project.