Both of these two colleges are tier-1 colleges. You can’t go wrong with either of them. One of my relatives who used to be a student of MANIT Bhopal speaks highly of the institution. According to her, you should prefer MANIT Bhopal to any other institution any day including BIT Mesra too.

Don’t take an educational loan to go to BIT Mesra, if you are getting MANIT Bhopal CSE. You can easily get an income-based scholarship at MANIT Bhopal. 

At MANIT placement percentage as well as the highest package, both are pretty high. At MANIT Bhopal, the placement percentage goes as high as 98% and the highest package offered this year was around 42 LPA. 

Hance, MANIT Bhopal is definitely is a better alternative.