Are there positions which cannot be properly analyzed by any computer? Are there positions in chess which every engines is unable to analyze
 properly ?

Maybe calm positions with a positional advantage the engines do not
 recognize ? Or positions won in the long term but with no concrete 
 winning moves ?
8/3k4/2p5/p2p2p1/P2P2P1/2KB4/8/8 w - - 0 1


In this position the engine gives advantage of around +2.5, but as you can see, this position is a draw as there is no way for white king to enter into Black's side of the board to penetrate any of the black pawns as the black pawns control all the accessible squares which are b4, c4, e4, f4 and h4. Even though white has an extra bishop it can only attack 2 of black pawns which are on c6 and d5. Taking the d5 pawn is recaptured by c6 pawn or taking the c6 first can be defended by the black king.

This is just an example of a position where an engine can give unfair advantage to a particular side though it isn't such. Here I'm not supposed to say the engine is making a mistake because it is programmed in such a way that it sees an extra bishop and with limited depth which is below 50 it says white has the advantage of extra bishop with no strings attached, hence gives you +2.5, but if you let it think up to the depth of 50 from this particular position (for which engine might take long time), it then shows it's a draw (0.00) because of the 50 move rule which is programmed into the engines.

With many examples as such, a simple concept of long term strategy can differentiate human brains from engines. As said by @jknappan in the first answer- openings are very hard for engines to evaluate, because the engines are purely based on mathematical calculations and it does not have it's own opening repertoire and humans do have because of the long term strategy.
A queens gambit or Sicilian is studied for a long time by great chess players and they understand what kind of middlegame it will turn into and how then it can turn into a playable advantage in the endgame ( unlike the above position though by having an advantage of 2.5 and yet not able to achieve a win in the endgame). These kind of long term strategies is not thinkable by chess engines.
One more concept of bishop pair can be taken into consideration to explain the difference between human thinking and chess engines. A good chess player would not wanna give up his bishop pair in the opening unless it gives him a very good advantage. But a computer would suggest you to play and give up the bishop pair even when it's calculations gives the slightest of 0.01 worth more of marginal advantage from its second line!
These are some of the positional strategies chess engines might miss to analyze but human studies do not.