How to improve my game I am doing tactics 30 minutes a day, practicing end games for about 90 minutes and analyzing 1 GM annotated game a day.

I can understand the logic behind why the move is played, but I can't apply it in my own game. I can't understand what the position is asking. I can know my opponent is making a mistake but I can't find a way to punish it.

My Elo rating is 1335. 

Are there any books to solve these problems?
Not any good books, as most use tactics as the only guide. however you can practice yourself.  Solitaire chess, where you try to guess the move--and the reason--before reading it from the annotated game, is the best practice, yet has the major flaw of not considering every style of play.

A must read for everyone is Nimzovitsch's My System.  Botvinnik's game are useful for showing how to maneuver, which is useful for exploiting positional mistakes.

Thinking Techniques (written by Dr. Ferguson ~ 1982)

BEFORE EVERY MOVE...THINK:


What new threat(s) has my opponent's last move created?  How can I answer it(them)?
Is my King safe?  Is my opponent threatening to checkmate in the next few moves?  Can I checkmate my opponent?
What threats can I set up?  How?
Have I seen this position or a similar one before?
If so:  who stands better, and what is the best plan for continuing?
If not:  what are the outstanding features and elements of this position, and what plan(s) and method(s) of achieving it are available?
What is my plan?  What specific position would I like to obtain?  How can I achieve my goal? How can I improve my position?
Which move is best?  Can I capture material without penalty? Can I employ an tactical device?
Is it safe to move my piece to the square I'm thinking about?
Did I remember to start my opponent's clock and write down my move?


Not as useful as I hoped, but without a game example or more definite  problems, it's hard to provide a specific answer.