I have the same problem, using two feeds to get shared feed items. Feed item content (description etc.) actually differ in my case, as they are different language versions. Only the item url is the same, and that makes them duplicates for the plugin.
In my opinion it should separate the feed items in database, even if the item url is the same. At least if the category is different between them.
I’m having a similar problem (separate thread in this forum), and I bet this is caused by how the plugin skips duplicate feed items.
It seems that even if you have separate feeds, but the source is same, it won’t import the items per feed, if the same feed item was imported from a different feed.
I think this needs some improvements for the duplicate checking logic. I bet we’re not the only ones struggling with this.