Properly mapped many-to-many collection should maintain "link table" transparently.

Could you post a code sample (your mapping at least)?

<?xml version="1.0" encoding="utf-8" ?>
<hibernate-mapping xmlns="urn:nhibernate-mapping-2.0" default-access="nosetter.camelcase">
<class name="QandADomainModel.QandAAuthenticationQuestion, QandADomainModel" table="QA_AUTHENTICATION_QUESTIONS" >
<id name="Id" column="QUESTION_ID" type="Int32" unsaved-value="0">
<generator class="native"/>
</id>
<property name="Text" column="TEXT" type="string" not-null="true" />
<property name="QuesLanguage" column="QUES_LANGUAGE" type="string" not-null="true" />
<property name="CreatedDate" column="CREATION_DATE" type="DateTime" not-null="true" />
<many-to-one name="QAClientApp" column="QA_CLIENT_APP_ID" class="QandADomainModel.QandAClientApplication, QandADomainModel" not-null="true" />
<property name="Status" column="STATUS" type="string" not-null="true" />
<bag name="QAAuthAnswers" lazy="false" inverse="false" cascade="all-delete-orphan" >
<key column="QUESTION_ID"/>
<one-to-many class="QandADomainModel.QandAAuthenticationAnswer, QandADomainModel"/>
</bag>
<bag name="QAUsers" table="QA_QUESTIONS_USERS" inverse="false" >
<key column="QUESTION_ID" />
<many-to-many column="USER_ID" class="QandADomainModel.QandAUser,QandADomainModel" />
</bag>
</class>

<class name="QandADomainModel.QandAUser, QandADomainModel" table="QA_USERS">
<id name="Id" type="Int32" column="USER_ID">
<generator class="native" />
</id>
<bag name="QAAuthenticationQuestions" table="QA_QUESTIONS_USERS" lazy="true" inverse="true" >
<key column="USER_ID" />
<many-to-many column="QUESTION_ID" class="QandADomainModel.QandAAuthenticationQuestion,QandADomainModel" />
</bag>
<property name="UserName" column="USER_NAME" type="String" />
<property name="CreationDate" column="CREATION_DATE" type="DateTime" />
<property name="Status" column="STATUS" type="String" />
<many-to-one name="QAClientApplication" column="CLIENT_APP_ID" class="QandADomainModel.QandAClientApplication, QandADomainModel" />
</class>

<class name="QandADomainModel.QandAClientApplication,QandADomainModel" table="QA_CLIENT_APPLICATIONS" >
<id name="Id" column="QA_CLIENT_APP_ID" type="Int32" unsaved-value="0" >
<generator class="native"/>
</id>

<property name="QAClientApplication" column="QA_CLIENT_APPLICATION_NAME" type="string" not-null="true" unique="true" />
<property name="KeyName" column="KEY_NAME" type="string" not-null="true" unique="true" />
<property name="CreatedDate" column="CREATION_DATE" type="DateTime" not-null="true" />
<property name="Status" column="STATUS" not-null="true" />
<bag name="QAAuthQuestions" lazy="false" inverse="true" cascade="all-delete-orphan" >
<key column="QA_CLIENT_APP_ID"/>
<one-to-many class="QandADomainModel.QandAAuthenticationQuestion,QandADomainModel"/>
</bag>
</class>

<class name="QandADomainModel.QandAAuthenticationAnswer, QandADomainModel" table="QA_AUTHENTICATION_ANSWERS" >
<id name="Id" column="ANSWER_ID" type="Int32" unsaved-value="0">
<generator class="native"/>
</id>
<property name="Text" column="TEXT" type="string" not-null="true" />
<many-to-one name="User" column="USER_ID" class="QandADomainModel.QandAUser, QandADomainModel" not-null="true" />
<many-to-one name="QAAuthQuestion" column="QUESTION_ID" class="QandADomainModel.QandAAuthenticationQuestion, QandADomainModel" not-null="true" />
<many-to-one name="QAClientApp" column="QA_CLIENT_APP_ID" class="QandADomainModel.QandAClientApplication, QandADomainModel" not-null="true" />
<property name="Status" column="STATUS" type="string" not-null="true" />
<property name="CreatedDate" column="CREATION_DATE" type="DateTime" />
<property name="LastModifiedDate" column="LAST_MODIFICATION_DATE" type="DateTime"/>
</class>
</hibernate-mapping>

First - I am not a many-to-many guru, but I have several such collections performing well in my apps. If I were you I would try the following:

- try cascade="all" at non-inverse end of collection
- make sure you are adding objects to collection at non-inverse end ( QandAAuthenticationQuestion1.QAUsers.Add(QandAUser1) )
- replace "bag" with "set" - bags are VERY ineffective here (the whole collection must be deleted and recreated in the db with every change)