Navmesh requirement for each agent and performance

I wanted to know if creating navmesh for each agent can cause some performance issues. Currently i upgraded my unity fro 2017.1 to 2017.2 and i got this warning on my working project after rebaking a navmesh.

"Failed to create agent because it is not close enough to the Navmesh" and lots of errors.

I used the default humanoid setup for all my agents and didn't got any issue so far. Everything worked well. If creating different mesh is a requirement for further updates, what would be the best solution for it ?

I would be grateful if anyone can suggest me a solution.