Sounds like you're flattening over a spot color. Stop flattening is the best answer. Turn on overprint preview is the second best.
When you place a file from Illustrator use either the AI file or a saved (not printed) PDF/X-4.
When you create a PDF from InDesign, don't print it, export it as PDF.
Never flatten graphics in Illustrator nor image layers in Photoshop. Why should you do so.
Never use EPS.
For InDesign's use you will never need crop marks. Leave them away, no one needs them.
Thanks for your help
I managed it. I´m sure its not the only solution. In Illustrator I flattened the transparency but check boxed the "Preserve Overprints and Spot Colours" instead of the "Preserve Alpha Tranparency" option. Then exported as PDF/X-4. I could then print from from Indesign, without the previous problems.
Willi. I need crop marks to guillotine the final printed material.
When you use AI files in InDesign you should NEVER flatten transparency in Illustrator. Why should you do so?
Because it was the only way I found to solve the problem.
Then you have the reason of the problem not solved yet.