( ... )
res = session.find("select ml, ms " +
         "from pt.comseal.arsol.vo.MpLote as ml join ml.mp as mp join ml.armazemMp, " +
         "pt.comseal.arsol.vo.MpStocks as ms " +
         "where mp.id = ms.mp.id and mp.referencia like upper('%" + ref + "%') order by ml.referencia asc");
( ... )

net.sf.hibernate.QueryException: undefined alias: pt [select ml from pt.comseal.arsol.vo.MpLote as ml join ml.mp as mp join ml.armazemMp, pt.comseal.arsol.vo.MpStocks as ms where mp.id = ms.mp.id and mp.referencia like upper('%refmp1%') order by ml.referencia asc]
   at net.sf.hibernate.hql.PathExpressionParser.token(PathExpressionParser.java:103)
   at net.sf.hibernate.hql.ParserHelper.parse(ParserHelper.java:29)
   at net.sf.hibernate.hql.FromParser.token(FromParser.java:193)
   at net.sf.hibernate.hql.ClauseParser.token(ClauseParser.java:87)
   at net.sf.hibernate.hql.PreprocessingParser.token(PreprocessingParser.java:123)
   at net.sf.hibernate.hql.ParserHelper.parse(ParserHelper.java:29)
   at net.sf.hibernate.hql.QueryTranslator.compile(QueryTranslator.java:149)
   at net.sf.hibernate.hql.QueryTranslator.compile(QueryTranslator.java:138)
( ... )

<?xml version="1.0"?>
<!DOCTYPE hibernate-mapping PUBLIC
    "-//Hibernate/Hibernate Mapping DTD 2.0//EN"
    "http://hibernate.sourceforge.net/hibernate-mapping-2.0.dtd" >
   
<hibernate-mapping>
<!--
    Created by Middlegen Hibernate plugin

    http://boss.bekk.no/boss/middlegen/
    http://hibernate.sourceforge.net/
-->

<class
    name="pt.comseal.arsol.vo.MpLote"
    table="mp_lote"
>

    <id
        name="id"
        type="long"
        column="id"
    >
        <generator class="increment" />
    </id>

    <property
        name="referencia"
        type="java.lang.String"
        column="referencia"
        not-null="true"
        length="-1"
    />

    <!-- associations -->
    <!-- bi-directional many-to-one association to Mp -->
    <many-to-one
        name="mp"
        class="pt.comseal.arsol.vo.Mp"
        not-null="true"
    >
        <column name="mp_fk" />
    </many-to-one>
   
    <!-- bi-directional one-to-one association to ArmazemMp -->
    <one-to-one
        name="armazemMp"
        class="pt.comseal.arsol.vo.ArmazemMp"
        outer-join="auto"
        constrained="false"
    />

</class>
</hibernate-mapping>

<?xml version="1.0"?>
<!DOCTYPE hibernate-mapping PUBLIC
    "-//Hibernate/Hibernate Mapping DTD 2.0//EN"
    "http://hibernate.sourceforge.net/hibernate-mapping-2.0.dtd" >
   
<hibernate-mapping>
<!--
    Created by Middlegen Hibernate plugin

    http://boss.bekk.no/boss/middlegen/
    http://hibernate.sourceforge.net/
-->

<class
    name="pt.comseal.arsol.vo.Mp"
    table="mp"
>

    <id
        name="id"
        type="long"
        column="id"
    >
        <generator class="increment" />
    </id>

    <property
        name="referencia"
        type="java.lang.String"
        column="referencia"
        not-null="true"
        length="-1"
    />
   
    <!-- associations -->
    <!-- bi-directional one-to-many association to MpLote -->
    <set
        name="mpLotes"
        lazy="true"
        inverse="true"
    >
        <key>
            <column name="mp_fk" />
        </key>
        <one-to-many
            class="pt.comseal.arsol.vo.MpLote"
        />
    </set>
   
    <!-- bi-directional one-to-many association to MpStock -->
    <set
        name="mpStocks"
        lazy="true"
        inverse="true"
    >
        <key>
            <column name="mp_fk" />
        </key>
        <one-to-many
            class="pt.comseal.arsol.vo.MpStock"
        />
    </set>

</class>
</hibernate-mapping>

( ... )
res = session.find("select ml, ms " +
         "from pt.comseal.arsol.vo.MpLote as ml join ml.mp as mp join ml.armazemMp as am, " +
         "pt.comseal.arsol.vo.MpStocks as ms " +
         "where mp.id = ms.mp.id and mp.referencia like upper('%" + ref_padrao + "%') order by ml.referencia asc");
( ... )

( ... )
res = session.find("select ml, ms " +
         "from pt.comseal.arsol.vo.MpLote as ml join ml.mp as mp join ml.armazemMp as am, " +
         "mp.MpStocks as ms " +
         "where mp.id = ms.mp.id and mp.referencia like upper('%" + ref + "%') order by ml.referencia asc");
( ... )