Bowser not doing Down B special at times...

[Zombie Saurian]

This is mostly happening in aerial attacks, while doing his Ground Pound Down B special, he instead uses his neutral B Fire instead. This has gotten me numerous occasions and resulted in death.

 

[Kaeldiar]

This is probably something on your end. Either you are miss-timing or there's something wrong with your controller, so that it doesn't always read

 

[Narpas_sword]

Unable to reproduce.
as above poster says.

Check with various controllers under a controlled environment where you're not likely to make mistakes.