This issue was reported at BAM-13631 and was supposedly fixed in 5.6.0.

Just tested this in Bamboo 5.9.3 and issue still exist.

Steps to replicate

1. Create an agent with NodeJS capability
2. Create an agent without NodeJS capability
3. Add the NodeJS task in a deployment environment task
4. Observe the number of agents capable of running the deployment

The agent without the NodeJS still shows as a capable agent.