Most of the agile problems I've seen have been organizations cargo-culting things they've read, rather than trying to actually be dexterous. Big-A agile versus, well, "agile".
Scrum has been the largest offender - squashing discussion in standups, allowing scrum to erode QA process, rote meetings that take 50% of the week, story points and refusing to discuss timetables in hours when absolutely needed, reporting status multiple times, having others estimate tasks who are not doing those tasks, etc.
These organizations that have done so have been some of the least agile, and waterfall-esque organizations can even be better. (They planned up front well, they changed a few minor things in the middle maybe, but cut out the overhead).
Scrum has been the largest offender - squashing discussion in standups, allowing scrum to erode QA process, rote meetings that take 50% of the week, story points and refusing to discuss timetables in hours when absolutely needed, reporting status multiple times, having others estimate tasks who are not doing those tasks, etc.
These organizations that have done so have been some of the least agile, and waterfall-esque organizations can even be better. (They planned up front well, they changed a few minor things in the middle maybe, but cut out the overhead).