Server problems.

I dont think you have any basic plugins like Essentials.
I advise you to download Essentials, EssentialsSpawn, and EssentialsProtect!

Does this have anything to do with my problem?

Yes because EssentialsSpawn has the option to protect spawn, and you can easily set that to :false.

Thanks, but I accidently left out a piece of information.
You can't plant saplings anywhere, near and away from spawn.

Ahhh, I'll think of something then lol

If bukkit.yml doesn't include that line, then delete it entirely and let it regenerate.

Here is an example bukkit.yml.

settings:
allow-end: true
warn-on-overload: true
spawn-radius: 16
permissions-file: permissions.yml
update-folder: update
ping-packet-limit: 25
use-exact-login-location: false
plugin-profiling: false
ticks-per:
animal-spawns: 400
monster-spawns: 1
auto-updater:
enabled: false
on-broken:
- warn-console
- warn-ops
on-update:
- warn-console
- warn-ops
preferred-channel: rb
host: dl.bukkit.org
suggest-channels: true
database:
username: bukkit
isolation: SERIALIZABLE
driver: org.sqlite.JDBC
password: walrus
url: jdbc:sqlite:{DIR}{NAME}.db
aliases:
icanhasbukkit:
- version