Command block and random normal block decay

Server is running off latest version of Spigot my problems are listed after the info here.

Plugin list and errors on loading for upfront information
OUR CURRENT PLUGINS

Bankcraft
CasinoSlots
ChestShop
Enjin Minecraft Plugin
Essentials
EssentialsChat (just a jar no folder)
EssentialsGroupManager (folder is assumed the GroupManger Plugin)
EssentialsSpawn (just a jar no folder)
Factions
iConomy
Lockette
mcore
MyHorse
NoCheatPlus
PluginMetics
PTweaks
SignShop
SimpleAutoMessage
SimpleHomes 2.0 (deleted realized essentials did the same)
SimpleRegionMarket
Spawner
update (folder seems to be empty is this safe to delete)
Updater
Votifier
Vault (just a jar no folder)
WarpPortals
Wither
WorldBorder
WorldEdit
WorldGuard
Buycraft (jar and folder been deleted)
Estate (jar and folder been deleted)
LiftSign (jar and folder been deleted)

Error's from consule during loading
20.11 18:04:10 [Server] WARNING API-only MCAccess: Some features will likely not function properly, performance might suffer.
20.11 18:04:26 [Server] WARNING Metrics error: ERR (IOException): Server returned HTTP response code: 502 for URL: http://report.mcstats.org/plugin/NoCheatPlus
20.11 18:04:10 [Server] WARNING Development builds: http://ci.ecocitycraft.com/job/NoCheatPlus/
20.11 18:04:10 [Server] WARNING Check for updates at BukkitDev: http://dev.bukkit.org/server-mods/nocheatplus/
20.11 18:04:10 [Server] WARNING API-only MCAccess: Some features will likely not function properly, performance might suffer.
20.11 18:04:10 [Server] WARNING Could not set up native access for your specific Minecraft + server-mod version.


Problem #1

Ok command blocks seem to work sometimes and sometimes they can be world-edited in but the commands reset every-time i click done (not cancel) i am making sure it's not a stupid/obvious mistake on my part. They ARE enabled in server.properties. I am not sure why i cant place them in but thats not the main problem because world-editing them in is fine with me. But them not keeping the commands like they WERE doing earlier prior to massive jar installing and removing. It has me boggled. Maybe it's in one of the plugins i listed configs' that i didn't check. I only really remember it in server properties and i believe in the essentials config it was listed and i believe its on allow. If there is anything i missed in configs that could help or just something i am doing wrong any help, or otherwise would be great.

Problem #2
Most people are going to jump to the conclusion mob spawning is allowed and this is ender-man's doings. But random blocks disappear at my spawn (it's so huge that there is no real chance mobs wonder into the mob spawning deny area. Anyway the problem is random blocks just disappear at times. Enderman-grief is deny on world-guard flags in the region. At first I thought it was some of my ranked players that had permission to the area just messing with me. But it's been at such random places that cant be the case. If anyone knows one of those plugins that cause that glitch or if its something common that Spigot servers have issues with. I would love to know. It's kinda driving me a bit nuts trying to figure out why. God forbid it starts doing it on our massive Redstone machines that are 5000+ Redstone. it will take a lifetime to trouble shoot them if this starts randomly taking out blocks around them.

You can come on the server if you want but blocks disappearing is not a common thing it happens quite a bit maybe 1 time a day i most likely just haven't noticed some areas that it happens at yet. Just assuming it could be more common then even i know about. I hope this info helps. These two odd problems been driving me up the wall. I appreciate any feedback. The ips in my signature.