Multimapped categories have different menu ids (bad for SEO)

It's great that flexicontent allows multimapping of items to various categories. However if you link to that same article which exists in two different categories through the menu, there are two different links created. This is an issue with SEO indexing where the same article will be indexed twice with two different URLs. Is there any way to get around this? I have an article named test in categories Main 1 and Main 2. I created two menu links (one to the main 1 category and 1 to the main 2 category) and I clicked on this item inside of each category.

It's the same item but the URL is different based on the menu item. Anybody have an idea on how to fix this?

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Multiple URLs for one content item is common throughout Joomla.
One core article linked from a menu, and from a module, and from another menu, and from a plug-in . . . all may have different URLs.
This is just more obvious in any component which does multi-mapping.

The only workaround is use an SEF component.
Components such as AceSEF and sh404SEF will map all the multiple URLs to one SEF URL.
For example the AceSEF extension for FLEXIcontent will map to the primary category link (as it should).
The SEF components also have features which enable manually fine tuning the URL mapping.
These components enable you to manage your URLs.

AceSEF has provided a free extension for FLEXIcontent.
An sh404SEF router was recently added to the FLEXIcontent core.

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thank you for your reply. I'm going to look into these two extensions further to see how they work.