I am currently writing a character that isn't who they claim to be. This character's true identity and affiliation will become known in the ending chapters. This character can be closely associated with Plutarch Heavensbee (Hunger Games Series) and Barty Crouch Jr (Harry Potter Series). Men who place themselves in high ranking positions only to give all that up for higher motives. How do I keep giving guesses to the reader without fully revealing the true person behind the facade too early on?
It all depends on your intention.
1) You want your reader to be suspicious about the character, but not know the true explanation. In this case you can put spotlight on this character, show some mystery and hidden depth, but leave a number of other possible explanations to his actions.
2) You want your reader to be totally oblivious, and only in last chapter smack his head - "How could I miss that?!" In this case you have to keep the spotlight somewhere else. The character should be fully consistent with his assumed identity, and if there's something strange going on, there always must be some other suspect.
In both cases you have to introduce the idea of a persona who is the real identity of your character. Shroud this persona in mystery, make the other characters look for him and try to learn about him without knowing that he is hiding in plain sight.
P.S. I think J. K. Rowling is using the idea of false identity too much, almost to the point that I know that newly introduced major characters are rarely the people they are pretending to be.
You can give people clues, but hide them as just strange or part of their character. For example, Barty Crouch Jr. (GoF spoiler)
drinks from a hip flask all the time, and keeps trying to help Harry with the Triwizard Tournament. The hip flask turns out to be Polyjuice Potion, and he is trying to make Harry win so he touches the cup first and gets sent to Voldemort.
These actions are explained as part of the character's paranoia and his caring nature. In the end, though, we realize that they are not part of his true nature, but rather part of his disguise/plot. When the character is revealed, the clues fall into place.
It's all bout the element of hiding important facts and creating smoke and mirrors. Not sure what your story is about, but you can have it so this character suddenly walks off when no one was looking and doesn't return. Gives them the element of being shady when really they went off for good reasons. The other key is to not give away the real information. Give enough to build the character, but mask some of the details. I think from HP Severus Snape would also be a good character that follows what you are looking for. They did a really great job of hiding his true self until the very end. All along we thought he was bad but ends up being a key hero.
It's all about perception and creating event points that, when only half of the information is present and the dots are not connected, make them appear to be one way, but then at the end, when they back track all the events and fill in the gaps, you are aware that your perception was wrong all this time.
Misdirection is a common method. When dealing with shady characters, people tend to pick one to hate above all others. Snape was mentioned, and people loved hating him. He was a character that was easy to hate. So you overlook Quirrel in Book 1.
This is highly dependent on your genre, though. In a detective story, having only one shady character almost always means there's either an open-and-shut case (not likely) or there's a subtly shady character. So you start questioning every character and their true motives (if you are genre savvy).
In the end, it all depends on how you want to handle your story. You, as omnipotent and omniscient author, should be able to weave the story in such a way that only what you want to show is shown, only what you want to hide is hidden. But to give a more in depth answer, I'd need more details of your story.
You can create a character that is a fraud, and seems to have inherent weaknesses, but once in a while they act out of character and against their supposed weakness, in some situation that is critical.
The reader will suspect the weakness is not really a weakness, and thus the character is a fraud, but nobody in-universe (unless you want them to) notices the fraud didn't fail.
In truth, the weakness is an adopted trait of the fraud they can use to conceal their covert actions or communications. I have seen this in movies before, the guy in a wheelchair is not disabled at all. But it doesn't have to be that dramatic; I have also seen the simpleton bumpkin janitor (mental weakness) turn out to be an expert multi-millionaire hacker.
Plutarch, that you mention, first meets Katniss at the palace dance; and in that dance he tells her, "being the head game maker has never been the most secure job in the world." She asks, "then why are you here?", and he responds "for the same reason as you, I volunteered." When she asks "Why?" he claims it was ambition, he wanted the games to mean something. She says they never meant anything, and he says "Maybe you inspired me to come back."
In other words, every time he is telling her the truth! But in an off-handed way, it is double speak. In watching the movie, it was at that moment I decided he was a double-agent:
"The same thing as you, I volunteered", was more than a surface truth, he was risking his life for love of a cause in the same way Katniss risked her life to save her sister.
"Ambition" was a misdirection, revealing his false weakness if taken as "personal ambition", which most would. But in a sense (I just realized) it was also a truth, his true ambition was altruistic, to overthrow Snow.
"I wanted the games to mean something" was a veiled truth, they would mean the end of dictator Snow.
And finally: Her courage in volunteering truly did inspire him to come back, to enter the lion's den.
His "weakness" of pretended personal ambition was enough to convince Snow and his crew that Plutarch's reason for volunteering was pure ambition. He was brutal and got people killed horribly in doing his game-maker job, but he was risking his own life and justified the casualties necessary to please Snow as acceptable losses.
Nevertheless (and perhaps because I write and know that every word in a screenplay should be meaningful) I decided he was probably an ally, I think even the choice to dance with Katniss was a clue. I admit I could not be certain he was a double-agent, I just couldn't think (as a writer) for any other purpose to that conversation, for chewing up three minutes of screen time for nothing.
Look for ways a "weakness" can be used to shield your double-life character, and let them speak the truth, albeit in veiled terms. Then trust your readers to put the pieces together.