I created a group "Resident" and stuck "/lp group Resident permission set essentials.tpa false" but the users can still use TPA.

Likewise I also added "essentials.gamemode" to "Engineer" and they cant use gm1

Other permissions seem to work fine, its just some of them that dont seem to stick

Are you sure your users have the group Resident? and the permission actually updated (/lp group resident permission info)

Are you using EssetialsX? https://github.com/drtshock/Essentials/wiki#differences-between-essentialsspigot-essentials-and-essentialsx