Upon completion I saw that there were about 49 cinimatics, yet not all of them play. You click to play, and it fades to black like it's going to play and the main menu just pops back up. They do not play in the game either, I replayed it again being very carefull and searchin. Some titels that don't work are:
"Scarecrow"
"Body Bag"
"Church Enterance"
There's some others also. Is this a glitch or something? Help if possible.

Where did you see those vids anyway? I've beaten the game and my list says 40 clips. Interestingly enough "Church Entrance" is an optional clip which only plays if you look at the church in chapter 3. I don't recall Scarecrow and Body Bag though, so maybe I missed them too. And for some reason none of these three clips can be viewed from my game's menu - despite the fact that I DID find the "Church Entrance". Do you remember seeing any of these clips when playing the game?

No, they never played at all in the game.

I've noticed the same problem too.
From the "View Cinematics" option it's obvious that game contains 49 movies, but there are only 40 movie files in corresponding game directory.
For example "Scarecrow" movie, mentioned in first post, has number 12 (numeration starts from '1') in "View Cinematics", but in movies directory corresponding video file *11.* ('11' because numeration starts from '0' there) is missing, that's why it can't be played.

Full list of cinematics that can't be played (numeration is started from '1'):
12. Scarecrow
15. Church Entrance
19. Big top
25. Cellar Entrance to House
31. World History Part 2 (*)
32. World History Part 3 (*)
33. Gravin's Wife (*)
39. Body Bag
41. Wall of Sorrow
(Cinematics that are marked with '*' sign are actually presented in "30. World History Part 1"/Mov029.smk).

This list corresponds to the list of missing *.smk files in data/vids directory (numeration is started from '000'):
Mov011.smk, Mov014.smk, Mov018.smk, Mov024.smk, Mov030.smk, Mov031.smk, Mov032.smk, Mov038.smk, Mov040.smk.

So is it possible to find these missing movie files somewhere? Or they are not exist at all.

I don't know about the missing cinematics in-game, but having compared with the original 3CD version I can safely say that no files are missing. There are exactly 40 files in the VIDS directory.

This one is done in-engine, I think (Scarecrow guarding Mother's house) There is a cinematic with asylum's chapel enterance... Doesn't this one play when you listen to Gavin's voice mail? This one sounds like the end boss introduction.