Student or Learner
1 "The project ended with a failure."
2 "The project ended in a failure."
Does 1 mean the project turned into a failure, and 2 mean the project ended during a failure?
3 "The project began with personnel changes."
4 "The project began in personnel changes."
Does 3 mean the project got started by firing and hiring people, and 4 mean the project ended during personnel changes?
(Not a Teacher)
1 suggests that there was a specific failure that ended the project, but overall, 1 & 2 mean the same thing. Also note that it's more common to say "The project ended in failure." with the 'a' being omitted.
You're assessment of 3 is correct. 4 doesn't make sense.