when use /clear [player] [banner|425] command from console, it dont remove banners...
Without Essentials all good with default clear command. (/clear [player] minecraft:banner -1 -1)

Essentials build 468
Spigot build 986 (MC 1.10.2)

Works for me on Essentials 2.0.1-b468. You are running quite an old version of spigot, so this might be the culprit. Have you tried deleting essentials configs and then rebooting the server?

does not work

Unable to reproduce on the latest version of Essentials. Please create a new issue if this is still a problem for you.