It is intended to work this way. The upload limit is a global usergroup restriction which means if you set they can not upload more than 3 images a day they can not. Now Optional Categories works by uploading a photo once to the one main category where the file is stored however there are 3 photo inserts in your database because it is treated like 3 separate photos which it should be. This is why you have the issue. You could theoretically modify your code in uploadphoto.php for upload restriction and alter your query. This would be outside the supported code and no support would be offered for it. But try adding this in bold in this query in the noted file.
Code:
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Upload to more tha one category 
Linear Mode
