Getting this spammed runnning v2.3.3 everytime someone logs in.

That doesn't help much. Please provide the full stacktrace.

I'm not getting any errors that I'm aware of, just that warning gets fired everytime someone logs in.

Alright, found out the errors were being stored in the EchoPet.log file.

[16/04/2014]---[01:38:23][EchoPet] §c[SEVERE] Failed to retrieve Pet data for Cthulu_Spawn in MySQL Database
com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column 'Owner' in 'where clause'
at sun.reflect.GeneratedConstructorAccessor150.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:407)
at com.mysql.jdbc.Util.getInstance(Util.java:382)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1052)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3593)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3525)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1986)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2140)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2626)
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2111)
at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2273)
at com.dsh105.echopet.libraries.bonecp.PreparedStatementHandle.executeQuery(PreparedStatementHandle.java:174)
at com.dsh105.echopet.api.SqlPetManager.createPetFromDatabase(SqlPetManager.java:132)
at com.dsh105.echopet.api.PetManager.loadPets(PetManager.java:56)
at com.dsh105.echopet.listeners.PetOwnerListener$1.run(PetOwnerListener.java:169)
at org.bukkit.craftbukkit.v1_7_R3.scheduler.CraftTask.run(CraftTask.java:67)
at org.bukkit.craftbukkit.v1_7_R3.scheduler.CraftScheduler.mainThreadHeartbeat(CraftScheduler.java:345)
at net.minecraft.server.v1_7_R3.MinecraftServer.v(MinecraftServer.java:628)
at net.minecraft.server.v1_7_R3.DedicatedServer.v(DedicatedServer.java:283)
at net.minecraft.server.v1_7_R3.MinecraftServer.u(MinecraftServer.java:576)
at net.minecraft.server.v1_7_R3.MinecraftServer.run(MinecraftServer.java:482)
at net.minecraft.server.v1_7_R3.ThreadServerApplication.run(SourceFile:628)

Seems like a mysql error, but I haven't changed anything?

Ah. You'll have to clear the existing table so that EchoPet can generate a new one. Due to the UUID changes I had to make in 2.3.x, the saving of data has now changed and is not compatible with tables generated with older versions of the plugin.

See that commit. Old SQL tables should now be migrated automatically.