Steps to confirm if predicted miRNA is good or bad
There won't be any duplicates in miRBase (for a given organism). Choose the taxon nearest to your organism if you are doing homology based discovery. If you want to take all/many organisms then you can use fastx_collapser to collapse redundant sequences. However you will lose the name of the miRNA. You can use awk also for this and it will keep the sequence header from the first organism in the list. 

awk '/&gt;/{$0=h} !(/&gt;/){if($0 in a){next} else{a[$0];print h"\n"$0}}' organism1.fa organism2.fa ... organismN.fa


Make sure that there are no extra newlines, otherwise you might need a small modification

To know if something is an expressed miRNA you would need to do a small RNA sequencing. There are some tools like mirdeep and mirSVR which you can use to discover miRNA sequences.