One things many people anticipated in Barack Obama's final days as president was that he would issue a last minute pardon of Hillary Clinton much in the way that Gerald Ford pardoned Richard Nixon. Then people who expected this were surprised when such an event did not happen. Some fans of Hillary Clinton tried to claim this lack of a pardon was based on her having done nothing deserving of a pardon, in spite of all the evidence to the contrary.
Given that the White House is inhabited by a Republican, and therefore the cabinet positions are Republican, and therefore the law enforcement apparatus is Republican, there is a good rason for Hillary Clinton to desire a pardon.
Then why would Barack Obama fail to pardon Hillary Clinton? One thing to consider is that in spite of them being in the same party and working together in the same administration, the two actually have never actually gotten along and actually do not like each other very much. His failure to pardon her could be due to him not wanting to do her any favors, as well as a punishment for her having failed to defeat Donald Trump in the general election.
Barack Obama has been shown that he can be quite petty. His behavior in escalating hostility with Russia is definitely an attempt to make things difficult for Donald Trump as he takes office. His failure to pardon Hillary Clinton could be even more petty than dislike. He could also be setting Hillary Clinton up for the uncomfortable position of being dependent on the good will of Donald Trump, making her dependent on his good will after a particularly vicious campaign. This would have the effect of making sure she behaves during the transition. She could have made this transition more difficult, but instead she had to stay on the good side of first Barack Obama and then Donald Trump. If she does anything to make things difficult for Donald Trump, he could always change his mind on the subject of legal activity against Hillary Clinton. This could be why she has been so completely out of the spot light since her defeat. She had no other choice.