Es ist ein fehler in der Permissions.yml,
hatte mal auch das gleiche Problem.
So sieht die Permissions.yml von meinem Server aus:

Edit zum Mitkopieren:
groups:
Gast:
default: true
prefix: '&d[Gast] '
permissions:
- chatmanager.chat.global
- modifyworld.login
- modifyworld.chat
Member:
permissions:
- essentials.warp
- essentials.sethome
- essentials.home
- essentials.spawn
prefix: '&c[Member] '
Admin:
permissions:
- '*'
prefix: '&a[Admin] '
Owner:
permissions:
- '*'
prefix: '&a[Owner] '
VIP:
permissions:
- essentials.warp
- essentials.spawn
- essentials.home
- essentials.sethome
- simpleregionmarket.*
- essentials.msg
- iconomy.money
prefix: '&1[VIP] '
Team:
permissions:
- essentials.warp
- essentials.spawn
- essentials.home
- essentials.sethome
- simpleregionmarket.*
- essentials.msg
- iconomy.money
- worldedit.*
- worldguard.*
- essentials.setwarp
- essentials.gamemode
prefix: '&b[Team] '
users:
Jonlinga:
group:
- Owner
Jorgo:
group:
- Owner
Kai:
group:
- Mod
- Moderator
- Member
Yusuke:
group:
- Owner
Pospiech:
group:
- Member
ProNeoXx:
group:
- Member
serVer96:
group:
- Member
Bananenbier:
group:
- Owner
VenomBlades:
group:
- Member
jason212:
group:
- Member
Player:
group:
- Member
Jynx404:
group:
- Member
NoXx_:
group:
- VIP
- Owner
- Member
linus:
group:
- Member
All_Stars_:
group:
- Owner
JustAFreak:
group:
- Member
BlackOut_:
group:
- Team
PortalPro:
group:
- Member
KnochenTener:
group:
- Member
I3l4CKHaWk:
group:
- Member
Dennis:
group:
- Member
Fabileidner:
group:
- Member
RolandHavana:
group:
- Member