Actually I haven't heard this. Does Arduino have a bunch of controversy now?
Some concerns are valid: Arduino doesn't have as much flexibility for digging really deep into things like pin and memory assignments and what happens when a microcontroller starts up. Also, the quality and documentation of Arduino support can vary from one MCU family to another.
There's a concern about the quality of libraries and code.
It doesn't support hardware debugging.
Granted, the embedded community has good reasons for being conservative, especially for critical applications.