Using PufferFsih 1.20.1-R0.1

[07:25:47] [Netty Epoll Server IO #2/ERROR]: Thread Netty Epoll Server IO #2 failed main thread check: Chunk getEntities call
java.lang.Throwable: null
at org.spigotmc.AsyncCatcher.catchOp(AsyncCatcher.java:15) ~[pufferfish-1.20.1.jar:git-Pufferfish-4]
at net.minecraft.server.level.ServerLevel.getEntities(ServerLevel.java:2579) ~[?:?]
at net.minecraft.server.level.ServerLevel.getEntityOrPart(ServerLevel.java:2036) ~[?:?]
at com.comphenix.protocol.reflect.accessors.DefaultMethodAccessor.invoke(DefaultMethodAccessor.java:23) ~[ProtocolLib.jar:?]
at com.comphenix.protocol.injector.EntityUtilities.getEntity(EntityUtilities.java:105) ~[ProtocolLib.jar:?]
at com.comphenix.protocol.injector.PacketFilterManager.getEntityFromID(PacketFilterManager.java:411) ~[ProtocolLib.jar:?]
at com.comphenix.protocol.wrappers.BukkitConverters$13.getSpecific(BukkitConverters.java:840) ~[ProtocolLib.jar:?]
at com.comphenix.protocol.wrappers.BukkitConverters$13.getSpecific(BukkitConverters.java:825) ~[ProtocolLib.jar:?]
at com.comphenix.protocol.reflect.StructureModifier.readInternal(StructureModifier.java:301) ~[ProtocolLib.jar:?]
at com.comphenix.protocol.reflect.StructureModifier.read(StructureModifier.java:251) ~[ProtocolLib.jar:?]
at main.java.me.dniym.listeners.pLisbListener$2.onPacketReceiving(pLisbListener.java:86) ~[IllegalStack-2.8.jar:?]
at com.comphenix.protocol.injector.SortedPacketListenerList.invokeReceivingListener(SortedPacketListenerList.java:122) ~[ProtocolLib.jar:?]
at com.comphenix.protocol.injector.SortedPacketListenerList.invokePacketRecieving(SortedPacketListenerList.java:75) ~[ProtocolLib.jar:?]
at com.comphenix.protocol.injector.PacketFilterManager.postPacketToListeners(PacketFilterManager.java:557) ~[ProtocolLib.jar:?]
at com.comphenix.protocol.injector.PacketFilterManager.invokePacketReceiving(PacketFilterManager.java:521) ~[ProtocolLib.jar:?]
at com.comphenix.protocol.injector.netty.manager.NetworkManagerInjector.onPacketReceiving(NetworkManagerInjector.java:118) ~[ProtocolLib.jar:?]
at com.comphenix.protocol.injector.netty.channel.NettyChannelInjector.processInboundPacket(NettyChannelInjector.java:500) ~[ProtocolLib.jar:?]
at com.comphenix.protocol.injector.netty.channel.InboundPacketInterceptor.channelRead(InboundPacketInterceptor.java:33) ~[ProtocolLib.jar:?]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:444) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:420) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:412) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.handler.codec.ByteToMessageDecoder.fireChannelRead(ByteToMessageDecoder.java:346) ~[netty-codec-4.1.87.Final.jar:4.1.87.Final]
at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:318) ~[netty-codec-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:444) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:420) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:412) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.handler.codec.ByteToMessageDecoder.fireChannelRead(ByteToMessageDecoder.java:346) ~[netty-codec-4.1.87.Final.jar:4.1.87.Final]
at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:318) ~[netty-codec-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:444) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:420) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:412) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.handler.codec.ByteToMessageDecoder.fireChannelRead(ByteToMessageDecoder.java:346) ~[netty-codec-4.1.87.Final.jar:4.1.87.Final]
at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:318) ~[netty-codec-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:444) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:420) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:412) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:103) ~[netty-codec-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:444) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:420) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:412) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.handler.timeout.IdleStateHandler.channelRead(IdleStateHandler.java:286) ~[netty-handler-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:442) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:420) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:412) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.handler.flush.FlushConsolidationHandler.channelRead(FlushConsolidationHandler.java:152) ~[netty-handler-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:442) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:420) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:412) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.DefaultChannelPipeline$HeadContext.channelRead(DefaultChannelPipeline.java:1410) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:440) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:420) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:919) ~[netty-transport-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.epoll.AbstractEpollStreamChannel$EpollStreamUnsafe.epollInReady(AbstractEpollStreamChannel.java:800) ~[netty-transport-classes-epoll-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.epoll.EpollEventLoop.processReady(EpollEventLoop.java:499) ~[netty-transport-classes-epoll-4.1.87.Final.jar:4.1.87.Final]
at io.netty.channel.epoll.EpollEventLoop.run(EpollEventLoop.java:397) ~[netty-transport-classes-epoll-4.1.87.Final.jar:4.1.87.Final]
at io.netty.util.concurrent.SingleThreadEventExecutor$4.run(SingleThreadEventExecutor.java:997) ~[netty-common-4.1.87.Final.jar:4.1.87.Final]
at io.netty.util.internal.ThreadExecutorMap$2.run(ThreadExecutorMap.java:74) ~[netty-common-4.1.87.Final.jar:4.1.87.Final]
at java.lang.Thread.run(Thread.java:833) ~[?:?]

The problem is in main.java.me.dniym.listeners.pLisbListener. If it is your own plugin, you need to change it such that getEntity is not updated asynchronously. Fork example, you can add the ListenerOption SYNC to the PacketAdapter.

Otherwise, please contact the developer of that plugin. It is no issue of ProtocolLib itself

Should be fixed in version 2.8.5+ of said plugin.