In the main storylines for both seasons, the writers make a point of having Will mention his sources.
In season 2, Will convinces Charlie to stick with the Genoa story, because he claims to have a source who also confirms the story.
In season 3, after Will convinces Neal to tell him the name of his source, he keeps referring to the person as a male, but everyone else thinks it is a female.
I kept waiting for this to become a storyline, but I just watched the finale, and nothing ever came of it.
I'm not sure I understand what you mean and what you try to understand.
I don't remember clearly what it was in season 2 but I remember I always had a feeling at the time that Will's and Charlie's source were actually the same person while they thought they had two different sources. But I can't remember clearly. So I'll let someone else answer that.
In season 3 I believe that Will using "he" to talk about his source was simply a red herring. That's why MacKenzie tells him at some point that he can stop saying He because she knows it's a woman. A woman as a source may have been easier to find (less women working for government agencies, etc.) as there would have been less suspects.
The staff were trying to cover their bases with the Genoa story, making sure they had enough "fact" to run it. Charlie had a source, and Will had a source - this would make 2 independent sources, and could therefore be reliable. I can't remember exactly how the scene went, but it was hinted to the audience that they were the same source (as in the same person, so therefore only 1 source, and not entirely reliable). Neither Charlie nor Will would say who their source was, and it was then revealed their source was the same person. A person who purposely misled them because he had a grudge against Charlie. This was supposed to be an example of "institutional failure" since (I guess) Charlie and Will should have known that it was the same person, and Charlie should have realized that he couldn't be trusted.
In season 3, I'm pretty sure Will was purposely saying "he" to not identify the source. As the other user said, a female agent would probably be easier to track down, but male would keep it more anonymous. It was revealed that the source was a female, but Will didn't want anyone else to be involved, so he kept saying "he" so Mac could not be tied to Will. He made a point in an episode that if he tells Mac anything, that Mac could be prosecuted alongside Will, and he wanted to make sure that didn't happen. By continually lying about the gender, then Will hasn't told Mac anything, and he's keeping her out of it.
In season two the lawyer asks (I think more than once) if anyone ever considered the possibility that Will's source and Charlie's source were the same person. It's never confirmed that they were the same person only pointed out as a possibility they should have considered.
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