The glitch is said to only happen in escape rooms (puzzle rooms) and can be avoided by simply not saving during them, they dont last that long either once you work out how to do the puzzle so its really not that needed to save during them and its pretty evident when you are about to go into one, thus you can prepare a save just before.
Is the game as good as 999? In my opinion, it is much much better.
The story is MUCH better, much more interesting and the twists in this game are fantastic, the characters are all solid and the writing (as expected) is exceptional. One thing the game has improved upon majorly from the last game is the puzzles, the puzzles are often very clever and really take some thinking to solve unlike the ones in 999, which could be solved with very little effort.
The only minor complaint anyone can have imo is that its not as "gory" as 999 was, but you cant complain about that if thats not what direction the game wanted to take. It more than makes up for it in other areas tho and the ally/betray parts of the game adds a great sense of involvement into the game, the choices you make determines how the rest of the game will play out.
Long story short, its awesome, get it.