Lowercase all phrases in the list (for easy comparison)
Remove phrases that have a length less than 3
Weight each phrase found in the previous steps as follows: Count the number of times the phrase appears in the document. If the phrase comes from Yahoo add 1 to the previous count (This favors Yahoo's presumed robustness). If the phrase does not come from Yahoo but if there are multiple terms in the phrase, add 2 to the previous count. (This assumes preference for multiple terms to single terms, if they did not come from Yahoo).
Remove phrases that are on the stop word list.
Remove phrases that are also part of a longer phrase in the list.
Sum the weight of all phrases obtained from all documents into one large list.
Rank the list.
The Issue Discovery tool is not designed to 'give proper weight' to items. It is more a heuristic, a data exploration tool rather than an empirical tool.