I upgraded my server with the same world I have been working with Pixelmon 5.0.4 and I moved to 5.1.0 and it keeps saying missing Id's and here is whats happening when it stops: 07.06 13:19:04 [Server] Server thread/INFO [FML]: Found a missing id from the world pixelmon:pixelmon.mob.chikoritaF
07.06 13:19:04 [Server] Server thread/INFO [FML]: Found a missing id from the world pixelmon:pixelmon.mob.horsea
07.06 13:19:04 [Server] Server thread/INFO [FML]: Found a missing id from the world pixelmon:pixelmon.mob.golurk
07.06 13:19:04 [Server] Server thread/INFO [FML]: Found a missing id from the world pixelmon:pixelmon.mob.squirtle
07.06 13:19:04 [Server] Server thread/INFO [FML]: Found a missing id from the world pixelmon:pixelmon.mob.turtwig
07.06 13:19:04 [Server] Server thread/INFO [FML]: Found a missing id from the world pixelmon:pixelmon.mob.kabuto
07.06 13:19:04 [Server] Server thread/INFO [FML]: Found a missing id from the world pixelmon:pixelmon.mob.chikoritaM
07.06 13:19:04 [Server] Server thread/INFO [FML]: Found a missing id from the world pixelmon:pixelmon.mob.diglett
07.06 13:19:04 [Server] Server thread/INFO [FML]: Found a missing id from the world pixelmon:pixelmon.mob.blastoise
07.06 13:19:04 [Server] Server thread/INFO [FML]: Found a missing id from the world pixelmon:pixelmon.mob.joltik
07.06 13:19:04 [Server] Server thread/INFO [FML]: Found a missing id from the world pixelmon:pixelmon.mob.latios
07.06 13:19:04 [Server] Server thread/INFO [FML]: Found a missing id from the world pixelmon:fig_berry
07.06 13:19:04 [Server] Server thread/INFO [FML]: Injecting existing block and item data into this server instance
07.06 13:19:04 [Server] Server thread/ERROR [fml.ModTracker]: This world was saved with mod pokexpmultiplier which appears to be missing, things may not work well
07.06 13:19:04 [Server] Server thread/INFO [fml.ModTracker]: This world was saved with mod pixelextras version 2.2.7 and it is now at version 2.2.8, things may not work well
07.06 13:19:04 [Server] Server thread/INFO [fml.ModTracker]: This world was saved with mod pixelmon version 5.0.4 and it is now at version 5.1.0, things may not work well


Ticket isn't wanting to go through with my plugin list so here they are:
AdminShop-1.10.2-1.8.2-universal.jar AutoBroadcasterSponge-0.2.1.jar BetterKits-0.9.6.jar ClearMob-1.3.2.jar EMPSponge.jar LuckPerms-Sponge-3.1.29.jar Nucleus-0.28.1-1.10.2-S5.1-plugin.jar PixelExtras-1.10.2-2.2.8-universal.jar Pixelmon-1.10.2-5.1.0-universal.jar PixelmonEconomyBridge-1.10.2-1.3.0.jar SilkTouch.jar SkyClaims-0.19.1-beta.jar TabManager-1.0.4.jar TotalEconomy-v1.5.3.jar griefprevention-1.10.2-2.3.1.293.jar holograms-2.2.jar spongeforge-1.10.2-2281-5.2.0-BETA-2292.jar votifier-sponge.jar worldedit-forge-mc1.11-6.1.6-dist.jar

I'm going to take a guess and say your pulling that log from a console that is being rate limited. *cough* multicrap *cough* Its waiting for you to type in '/fml confirm' to allow forge to continue loading the world even with missing items.